Update puma #286
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Update puma #286
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fixing tests in #283 |
marouenbg
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Jun 2, 2023
* add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>
marouenbg
added a commit
that referenced
this pull request
Sep 2, 2023
* 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>
marouenbg
added a commit
that referenced
this pull request
Sep 18, 2023
* 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method * Exported COBRA and improved description --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>
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Nov 26, 2023
* add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Added COBRA method (#293) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Update README.md * Update TIGER (#297) * Smaller changes in COBRA (#296) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method * Exported COBRA and improved description --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Cobra docs (#298) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add cobra docs * build new website * update package * update package * add package * export pandaR classes * add site html * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * Update README.md * Update main.yml * Update main.yml * Update main.yml * Fixed dependency on uchardet (#301) * Fixed dependency on uchardet * Removed RCy3 from Imports * Added RCy3 back to Imports * Feature: included pcor decomposition natively in cobra (#299) * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Update COBRA.R --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update README.md --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> Co-authored-by: Soel Micheletti <soel.micheletti@hotmail.it> Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
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* add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Added COBRA method (#293) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Update README.md * Update TIGER (#297) * Smaller changes in COBRA (#296) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method * Exported COBRA and improved description --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Cobra docs (#298) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add cobra docs * build new website * update package * update package * add package * export pandaR classes * add site html * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * Update README.md * Update main.yml * Update main.yml * Update main.yml * Fixed dependency on uchardet (#301) * Fixed dependency on uchardet * Removed RCy3 from Imports * Added RCy3 back to Imports * Feature: included pcor decomposition natively in cobra (#299) * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Update COBRA.R --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update README.md * Fix dragon (#306) * add DRAGON outline * implemented vars and esqs, added tests * added optim * Added fn to get shrunken cov and unit tests * Update DESCRIPTION * Update DESCRIPTION * mechanics for prec mat and parcor * added testdata directory * fixed test paths * Update test-dragon.R * added export function and tests * updated docs * added ex datasets * fixed bug w/self-edges in GGM * fixed GGM diagonal issue * fixed merge conflicts in docs * fixed more merge conflicts * Fix 309 (#310) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix 309 * Update README.md * Aadd yarn (#314) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add yarn * add yarn * add yarn * change yarn vignette * change yarn vignette * change yarn vignette * add download data set * add download data set * update yarn * update yarn * update yarn * update yarn * add download file * add download file * add download file * update workflow * update workflow * update to R 4.3 * update to R 4.3 * Add monster desc (#312) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add monster description --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> Co-authored-by: Soel Micheletti <soel.micheletti@hotmail.it> Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
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this pull request
Jun 8, 2024
* add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Added COBRA method (#293) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Update README.md * Update TIGER (#297) * Smaller changes in COBRA (#296) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method * Exported COBRA and improved description --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Cobra docs (#298) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add cobra docs * build new website * update package * update package * add package * export pandaR classes * add site html * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * Update README.md * Update main.yml * Update main.yml * Update main.yml * Fixed dependency on uchardet (#301) * Fixed dependency on uchardet * Removed RCy3 from Imports * Added RCy3 back to Imports * Feature: included pcor decomposition natively in cobra (#299) * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Update COBRA.R --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update README.md * Fix dragon (#306) * add DRAGON outline * implemented vars and esqs, added tests * added optim * Added fn to get shrunken cov and unit tests * Update DESCRIPTION * Update DESCRIPTION * mechanics for prec mat and parcor * added testdata directory * fixed test paths * Update test-dragon.R * added export function and tests * updated docs * added ex datasets * fixed bug w/self-edges in GGM * fixed GGM diagonal issue * fixed merge conflicts in docs * fixed more merge conflicts * Fix 309 (#310) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix 309 * Update README.md * Aadd yarn (#314) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add yarn * add yarn * add yarn * change yarn vignette * change yarn vignette * change yarn vignette * add download data set * add download data set * update yarn * update yarn * update yarn * update yarn * add download file * add download file * add download file * update workflow * update workflow * update to R 4.3 * update to R 4.3 * Add monster desc (#312) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add monster description --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> Co-authored-by: Soel Micheletti <soel.micheletti@hotmail.it> Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
marouenbg
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Jul 26, 2024
* update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Added COBRA method (#293) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Update README.md * Update TIGER (#297) * Smaller changes in COBRA (#296) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method * Exported COBRA and improved description --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Cobra docs (#298) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add cobra docs * build new website * update package * update package * add package * export pandaR classes * add site html * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * Update README.md * Update main.yml * Update main.yml * Update main.yml * Fixed dependency on uchardet (#301) * Fixed dependency on uchardet * Removed RCy3 from Imports * Added RCy3 back to Imports * Feature: included pcor decomposition natively in cobra (#299) * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Update COBRA.R --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update README.md * Fix dragon (#306) * add DRAGON outline * implemented vars and esqs, added tests * added optim * Added fn to get shrunken cov and unit tests * Update DESCRIPTION * Update DESCRIPTION * mechanics for prec mat and parcor * added testdata directory * fixed test paths * Update test-dragon.R * added export function and tests * updated docs * added ex datasets * fixed bug w/self-edges in GGM * fixed GGM diagonal issue * fixed merge conflicts in docs * fixed more merge conflicts * Fix 309 (#310) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix 309 * Update README.md * Aadd yarn (#314) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add yarn * add yarn * add yarn * change yarn vignette * change yarn vignette * change yarn vignette * add download data set * add download data set * update yarn * update yarn * update yarn * update yarn * add download file * add download file * add download file * update workflow * update workflow * update to R 4.3 * update to R 4.3 * Add monster desc (#312) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add monster description * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * BLOBFISH Implementation (#321) * Added BLOBFISH * Removed singleton genes in BLOBFISH output * Added export statement to method for plotting networks * Added the ability to highlight the 2-hop subnetwork * Modified null distribution to include entire prior * Moved the significance testing to the beginning and added FDR adjustment * Moved calculation of p-values to a separate function * Updated tests for BLOBFISH * Added color-coding functionality to the plots * Delete tests/testthat/test-blobfish.R Deleted the test file as requested to see if we are able to build. * Fixed devtools::check() warnings and notes * First commit * man/cobra.Rd * Added tests back * Fixed warnings in build * Removed local import * Added description of BLOBFISH to the README * Fixed the Errors in pkgdown Website Build (#323) * Added missing references from BLOBFISH and YARN * Added data for YARN vignettes to YAML reference * Added documentation generated during pkgdown build * Changed VignetteIndexEntry fields to match titles in YAML file to address mismatch warnings * Removed PNG files * Added the PNG files back * Added PNG files back in --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> Co-authored-by: Soel Micheletti <soel.micheletti@hotmail.it> Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
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