v1.5.4 (#304) · netZoo/netZooR@2aa1073

Commit

v1.5.4 (#304)

* 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>

Loading branch information

10 people authored Nov 26, 2023

1 parent ac22884 commit 2aa1073

.github/workflows/main.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -34,7 +34,7 @@ jobs:
  
        steps:

          - uses: actions/checkout@v2

          - uses: actions/checkout@v3

            with:

              token: ${{ secrets.GITHUB_TOKEN }}

    @@ -48,7 +48,7 @@ jobs:
  
          - name: install dependencies

            uses: r-lib/actions/setup-r-dependencies@v2

            with:

              cache-version: 1

              cache-version: 2

              extra-packages: |

                 any::reticulate

                 any::rcmdcheck

    @@ -63,6 +63,14 @@ jobs:
  
                extSoftVersion()["BLAS"]

            shell: Rscript {0}

          - if: matrix.os == 'ubuntu-latest'

            run: |

              sudo apt-get install python3-venv

              pip install --upgrade pip

              python3 -m venv env

              source env/bin/activate

              echo "VIRTUAL ENV:" $VIRTUAL_ENV

          - name: Install reticulate

            run: |

                library("reticulate")

DESCRIPTION

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1,8 +1,8 @@
  
    Package: netZooR

    Type: Package

    Title: Unified methods for the inference and analysis of gene regulatory networks

    Version: 1.4.0

    Date: 2023-06-03

    Version: 1.5.4

    Date: 2023-09-25

    Authors@R: c(person("Marouen", "Ben Guebila",

    			email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),

    	     person("Tian", "Wang", 

    @@ -24,11 +24,13 @@ Description: netZooR unifies the implementations of several Network Zoo methods
  
    Depends: R (>= 4.2.0),

       	 igraph,

    	 reticulate,

             pandaR,

             yarn,

    	 pandaR,

             matrixcalc

    Remotes: 

    	 stan-dev/cmdstanr 

    	 stan-dev/cmdstanr,

    	 jnpaulson/pandaR, 

    	 cytoscape/RCy3

    biocViews:

    	 NetworkInference,

    	 Network,

    @@ -37,8 +39,8 @@ biocViews:
  
             Transcription, 

             Microarray,   

             GraphAndNetwork

    Imports: 

        RCy3,

    Imports:

        RCy3, 

        viridisLite,

        STRINGdb,

        Biobase,

    @@ -69,9 +71,11 @@ Imports:
  
        methods,

        dplyr,

        graphics,

    	cmdstanr,

        cmdstanr,

        GeneNet,

        loo

        loo,

        rARPACK,

        corpcor

    License: GPL-3

    Encoding: UTF-8

    LazyData: false

NAMESPACE

-Original file line number
+Diff line change
@@ -1,11 +1,11 @@
     # Generated by roxygen2: do not edit by hand
-    export(TIGER)
     export(adj2el)
     export(adj2regulon)
     export(alpaca)
     export(alpacaCrane)
     export(alpacaExtractTopGenes)
+    export(cobra)
     export(condorCluster)
     export(condorCoreEnrich)
     export(condorMatrixModularity)
@@ Expand Down Expand Up / @@ -41,12 +41,13 @@ export(pandaDiffEdges) @@
     export(pandaPy)
     export(pandaToAlpaca)
     export(pandaToCondorObject)
-    export(prior.pp)
+    export(priorPp)
     export(puma)
     export(runEgret)
     export(sambar)
     export(sourcePPI)
     export(spider)
+    export(tiger)
     export(visPandaInCytoscape)
     import(AnnotationDbi, except= select)
@@ Expand Down @@

R/COBRA.R

-Original file line number
+Diff line change
@@ -0,0 +1,82 @@
+    #' Run COBRA in R
+    #'
+    #' Description:
+    #'               COBRA decomposes a (partial) gene co-expression matrix as a
+    #'               linear combination of covariate-specific components.
+    #'               It can be applied for batch correction, differential co-expression
+    #'               analysis controlling for variables, and to understand the impact of
+    #'               variables of interest to the observed co-expression.
+    #'
+    #' Inputs:
+    #' @param X               : design matrix of size (n, q), n = number of samples, q = number of covariates
+    #' @param expressionData  : gene expression as a matrix of size (g, n), g = number of genes
+    #' @param method     : if pearson, the decomposition of the co-expression matrix is compouted. If pcorsh, COBRA decomposes the regularized partial co-expression
+    #'
+    #' Outputs:
+    #' @return psi : impact of each covariate on the eigenvalues as a matrix of size (q, n)
+    #' @return Q   : eigenvectors corresponding to non-zero eigenvalues as a matrix of size (g, n)
+    #' @return D   : non-zero eigenvalues as a list of length n
+    #' @return G   : (standardized) gene expression as a matrix of size (g, n)
+    #'
+    #' @examples
+    #'
+    #' g <- 100 # number of genes
+    #' n <- 10 # number of samples
+    #' q <- 2 # number of covariates
+    #' X <- X <- cbind(rep(1, n), rbinom(n, 1, 0.5))
+    #' expressionData=matrix(rnorm(g*n, 1, 1), ncol = n, nrow = g)
+    #'
+    #' # Run COBRA algorithm
+    #' cobra_output <- cobra(X, expressionData)
+    #'
+    #' @export
+    cobra <- function(X, expressionData, method = "pearson"){
+      if(!(method %in% c("pearson", "pcorsh", "dragon"))){
+        stop("Only Pearson and pcor methods are supported. Please make sure to provide a valid method argument.")
+      }
+      numSamples <- ncol(expressionData)
+      if(method != "dragon"){
+        N <- min(ncol(expressionData),nrow(expressionData))
+      }
+      C <- 0
+      if(method == "pearson"){
+        G_star <- expressionData-rowMeans(expressionData)
+        expressionData <- (G_star/sqrt(rowSums(G_star^2)))
+        expressionData <- as.matrix(expressionData)
+        C <- tcrossprod(expressionData)
+      }
+      if(method == "dragon"){
+        if(length(expressionData) != 2){
+          stop("Dragon needs two layers, please provide a list of two matrices in expressionData or consider using the pcorsh argument")
+        }
+        if(dim(expressionData[[1]])[2] != dim(expressionData[[2]])[2]){
+          stop("Dragon layers in expressionData list must have the same number of samples")
+        }
+        C <- dragon(t(expressionData[[1]]), layer2 = t(expressionData[[2]]), pval=FALSE)$cov
+        N <- dim(expressionData[[1]])[2]
+        numSamples <- N
+        expressionData <- rbind(expressionData[[1]], expressionData[[2]])
+        print(dim(expressionData))
+      }
+      if(method == "pcorsh"){
+       C <- matrix(as.numeric(pcor.shrink(t(expressionData))), dim(expressionData)[1], dim(expressionData)[1])
+      }
+      eigenG <- rARPACK::eigs_sym(C,N)
+      Q <- eigenG$vectors
+      D <- diag(eigenG$values)
+      hatmat <- ginv(crossprod(X))%*%t(X)
+      Qinv <- ginv(Q)
+      QinvG <- Qinv%*%(expressionData)
+      est <- t(sapply(seq_len(nrow(hatmat)), function(hatmatRow){
+        diag(QinvG%*%(numSamples*diag(hatmat[hatmatRow,]))%*%t(QinvG))
+      }))
+      list(psi=est, Q=Q, D=eigenG$values, G=expressionData)
+    }

R/PANDA.R

Original file line number	Diff line number	Diff line change
Expand Up		@@ -201,4 +201,3 @@ pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu",
		return(output)
		}

R/PUMA.R

-Original file line number
+Diff line change
@@ Expand Up @@
       pandaObj(regNet=regulatoryNetwork, coregNet=geneCoreg, coopNet=tfCoopNetwork, numGenes=numGenes, numTFs=numTFs, numEdges=numEdges)
     }
-    pandaObj <- setClass("panda", slots=c("regNet","coregNet","coopNet","numGenes","numTFs","numEdges"))
-    setMethod("show","panda",function(object){print.panda(object)})

R/SPIDER.R

-Original file line number
+Diff line change
@@ Expand Up @@
         resList$coopNet <- tfCoopNetwork
       }
       pandaObj(regNet=regulatoryNetwork, coregNet=geneCoreg, coopNet=tfCoopNetwork, numGenes=numGenes, numTFs=numTFs, numEdges=numEdges)
-    }
-    pandaObj <- setClass("panda", slots=c("regNet","coregNet","coopNet","numGenes","numTFs","numEdges"))
-    setMethod("show","panda",function(object){print.panda(object)})
+    }

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