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netZooR v1.6.0 #324

Merged
merged 261 commits into from
Jul 26, 2024
Merged

netZooR v1.6.0 #324

merged 261 commits into from
Jul 26, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jan 29, 2022

  1. update workfolw

    @marouenbg
    marouenbg committed Jan 29, 2022
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  2. update workfolw

    @marouenbg
    marouenbg committed Jan 29, 2022
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  3. update workfolw

    @marouenbg
    marouenbg committed Jan 29, 2022
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  4. update workfolw

    @marouenbg
    marouenbg committed Jan 29, 2022
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  5. Update main.yml

    @marouenbg
    marouenbg authored Jan 29, 2022
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  6. Update main.yml

    @marouenbg
    marouenbg authored Jan 29, 2022
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  7. Update main.yml

    @marouenbg
    marouenbg authored Jan 29, 2022
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Commits on Jan 30, 2022

  1. Merge pull request #236 from marouenbg/fix-crane-alpaca 

    update crane
    @marouenbg
    marouenbg authored Jan 30, 2022
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Commits on Feb 15, 2022

  1. fix lioness py

    @marouenbg
    marouenbg committed Feb 15, 2022
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  2. udpate lioness in R

    @marouenbg
    marouenbg committed Feb 15, 2022
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Commits on Feb 16, 2022

  1. include calculations python

    @marouenbg
    marouenbg committed Feb 16, 2022
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Commits on Feb 17, 2022

  1. update panda rm missing

    @marouenbg
    marouenbg committed Feb 17, 2022
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  2. update panda

    @marouenbg
    marouenbg committed Feb 17, 2022
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  3. update lioness joblib

    @marouenbg
    marouenbg committed Feb 17, 2022
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  4. revert commits

    @marouenbg
    marouenbg committed Feb 17, 2022
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  5. fix conflcit

    @marouenbg
    marouenbg committed Feb 17, 2022
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  6. ALPACA fix to NAs in community assignement

    @marouenbg
    marouenbg committed Feb 17, 2022
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Commits on Feb 18, 2022

  1. version bump

    @marouenbg
    marouenbg committed Feb 18, 2022
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  2. Merge pull request #238 from marouenbg/upgrade-alpaca 

    ALPACA fix to NAs in community assignment
    @marouenbg
    marouenbg authored Feb 18, 2022
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  3. revert lioness

    @marouenbg
    marouenbg committed Feb 18, 2022
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  4. update crane with alpaca changes

    @marouenbg
    marouenbg committed Feb 18, 2022
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  5. update lioness

    @marouenbg
    marouenbg committed Feb 18, 2022
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  6. Merge pull request #239 from marouenbg/update-crane 

    update crane with alpaca changes
    @marouenbg
    marouenbg authored Feb 18, 2022
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  7. update lioness python

    @marouenbg
    marouenbg committed Feb 18, 2022
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  8. fix test

    @marouenbg
    marouenbg committed Feb 18, 2022
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  9. update workflows

    @marouenbg
    marouenbg committed Feb 18, 2022
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Commits on Feb 19, 2022

  1. put back github actions

    @marouenbg
    marouenbg committed Feb 19, 2022
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  2. Merge pull request #237 from marouenbg/fix-panda-py 

    fix lioness py
    @marouenbg
    marouenbg authored Feb 19, 2022
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Commits on Feb 22, 2022

  1. Fixed typo

    Kate Hoff Shutta committed Feb 22, 2022
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Commits on Feb 25, 2022

  1. Added LIONESS-pearson option + unit test

    Kate Hoff Shutta committed Feb 25, 2022
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  2. Merge branch 'kate-dev' of https://github.com/katehoffshutta/netZooR … 

    …into kate-dev
    Kate Hoff Shutta committed Feb 25, 2022
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  3. changed param labels in LIONESS example

    Kate Hoff Shutta committed Feb 25, 2022
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Commits on Feb 28, 2022

  1. updated docs for lioness() function

    Kate Hoff Shutta committed Feb 28, 2022
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Commits on Mar 1, 2022

  1. Update main.yml

    @marouenbg
    marouenbg authored Mar 1, 2022
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  2. Merge branch 'devel' into kate-dev

    @marouenbg
    marouenbg authored Mar 1, 2022
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  3. Update main.yml

    @marouenbg
    marouenbg authored Mar 1, 2022
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  4. Merge pull request #241 from katehoffshutta/kate-dev 

    Kate dev
    @marouenbg
    marouenbg authored Mar 1, 2022
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Commits on Apr 26, 2022

  1. bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

    @nturaga
    nturaga committed Apr 26, 2022
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  2. bump x.y.z version to odd y following creation of RELEASE_3_15 branch

    @nturaga
    nturaga committed Apr 26, 2022
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Commits on Jun 10, 2022

  1. Update DESCRIPTION

    @marouenbg
    marouenbg authored Jun 10, 2022
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Commits on Jun 16, 2022

  1. fix crane issue #240

    @marouenbg
    marouenbg committed Jun 16, 2022
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  2. Merge pull request #244 from marouenbg/fix-crane 

    fix crane issue #240
    @marouenbg
    marouenbg authored Jun 16, 2022
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Commits on Jun 23, 2022

  1. expanded PANDA and LIONESS description

    @katehoffshutta
    katehoffshutta committed Jun 23, 2022
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Commits on Jun 24, 2022

  1. update crane fix

    @marouenbg
    marouenbg committed Jun 24, 2022
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  2. added ALPACA, EGRET, and OTTER descriptions

    @katehoffshutta
    katehoffshutta committed Jun 24, 2022
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  3. Update README.md

    @katehoffshutta
    katehoffshutta authored Jun 24, 2022
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  4. Merge pull request #245 from marouenbg/fix-crane-2 

    update crane fix
    @marouenbg
    marouenbg authored Jun 24, 2022
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Commits on Jun 27, 2022

  1. typo in na.rm

    @marouenbg
    marouenbg committed Jun 27, 2022
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  2. Merge pull request #246 from marouenbg/fix-crane-3 

    typo in na.rm
    @marouenbg
    marouenbg authored Jun 27, 2022
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  3. update workflow

    @marouenbg
    marouenbg committed Jun 27, 2022
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  4. update workflow2

    @marouenbg
    marouenbg committed Jun 27, 2022
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  5. fix-actions-3

    @marouenbg
    marouenbg committed Jun 27, 2022
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  6. add r lib v2

    @marouenbg
    marouenbg committed Jun 27, 2022
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  7. add r lib v2

    @marouenbg
    marouenbg committed Jun 27, 2022
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Commits on Jun 28, 2022

  1. update condor test

    @marouenbg
    marouenbg committed Jun 28, 2022
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  2. update condor test

    @marouenbg
    marouenbg committed Jun 28, 2022
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  3. update condor test

    @marouenbg
    marouenbg committed Jun 28, 2022
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  4. update condor test

    @marouenbg
    marouenbg committed Jun 28, 2022
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  5. show testthat output

    @marouenbg
    marouenbg committed Jun 28, 2022
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  6. add pandoc and use cache

    @marouenbg
    marouenbg committed Jun 28, 2022
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  7. use built in check

    @marouenbg
    marouenbg committed Jun 28, 2022
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  8. use built in check

    @marouenbg
    marouenbg committed Jun 28, 2022
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  9. update actions with built in check

    @marouenbg
    marouenbg committed Jun 28, 2022
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  10. bump version

    @marouenbg
    marouenbg committed Jun 28, 2022
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  11. use built in coverage

    @marouenbg
    marouenbg committed Jun 28, 2022
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  12. use built in coverage

    @marouenbg
    marouenbg committed Jun 28, 2022
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  13. remove sudo

    @marouenbg
    marouenbg committed Jun 28, 2022
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  14. update actions

    @marouenbg
    marouenbg committed Jun 28, 2022
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  15. update actions

    @marouenbg
    marouenbg committed Jun 28, 2022
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  16. removed sudo from actions

    @marouenbg
    marouenbg committed Jun 28, 2022
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  17. ugrade to R42

    @marouenbg
    marouenbg committed Jun 28, 2022
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  18. remove virtualenv

    @marouenbg
    marouenbg committed Jun 28, 2022
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  19. remove virtualenv

    @marouenbg
    marouenbg committed Jun 28, 2022
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  20. remove virtualenv

    @marouenbg
    marouenbg committed Jun 28, 2022
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Commits on Jun 29, 2022

  1. modify condor test

    @marouenbg
    marouenbg committed Jun 29, 2022
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  2. update condor test

    @marouenbg
    marouenbg committed Jun 29, 2022
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  3. update condor test

    @marouenbg
    marouenbg committed Jun 29, 2022
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  4. adding retiucualte to covr

    @marouenbg
    marouenbg committed Jun 29, 2022
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  5. adding retiucualte to covr

    @marouenbg
    marouenbg committed Jun 29, 2022
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  6. add panda test to coverignore

    @marouenbg
    marouenbg committed Jun 29, 2022
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  7. update actions

    @marouenbg
    marouenbg committed Jun 29, 2022
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  8. remove lioness tests from coverage

    @marouenbg
    marouenbg committed Jun 29, 2022
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  9. remove lioness tests from coverage

    @marouenbg
    marouenbg committed Jun 29, 2022
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  10. added MONSTER and SAMBAR

    @katehoffshutta
    katehoffshutta committed Jun 29, 2022
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  11. Merge branch 'master' of https://github.com/katehoffshutta/netZooR

    @katehoffshutta
    katehoffshutta committed Jun 29, 2022
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  12. remove lionessR test

    @marouenbg
    marouenbg committed Jun 29, 2022
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  13. Added CONDOR and YARN

    @katehoffshutta
    katehoffshutta committed Jun 29, 2022
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  14. Update README.md

    @katehoffshutta
    katehoffshutta authored Jun 29, 2022
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  15. Merge branch 'devel' into master

    @marouenbg
    marouenbg authored Jun 29, 2022
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  16. put back otter in rbuild

    @marouenbg
    marouenbg committed Jun 29, 2022
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  17. remove condor test

    @marouenbg
    marouenbg committed Jun 29, 2022
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Commits on Jun 30, 2022

  1. remove condor test

    @marouenbg
    marouenbg committed Jun 30, 2022
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  2. remove lioness docs

    @marouenbg
    marouenbg committed Jun 30, 2022
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  3. add lioness to buildingore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  4. donttest lionesss

    @marouenbg
    marouenbg committed Jun 30, 2022
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  5. remove coverage from ubuntu test

    @marouenbg
    marouenbg committed Jun 30, 2022
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  6. remove rbuilignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  7. update rbuildignore

    @marouenbg
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  8. update rbuildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  9. update rbuildignore

    @marouenbg
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  10. update rbuildignore

    @marouenbg
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  11. update rbuildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  12. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  13. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  14. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  15. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  16. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  17. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  18. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  19. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  20. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  21. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  22. put back tests

    @marouenbg
    marouenbg committed Jun 30, 2022
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  23. add padanedge diff test

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  24. add back egeret test

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  25. add monster test

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Commits on Jul 1, 2022

  1. fix monster test

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  2. tolerance in expect equal

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  3. tolerance in expect equal

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  6. add sourceppi

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  7. fixed PANDA tests

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  1. modify panda test

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  2. update lioness test

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  3. fix expect message

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  1. reduced lioness test data

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  6. Merge pull request #247 from marouenbg/fix-actions 

    update GitHub actions workflow
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  7. Merge pull request #248 from katehoffshutta/master 

    Extended zoo animal descriptions on readme
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  1. fix desc

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  2. updating bioc (#250) 

    * updating bioc

* remove empty lines

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  3. Merge branch 'master' into devel

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  4. Merge branch 'master' of https://github.com/netZoo/netZooR

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  5. update citation

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  1. Update README.md

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  2. update lioness test

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  3. removed two last lioness tests

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  4. removed two last lioness tests

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  5. removed two last lioness tests

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  6. no saving of lioness networks

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  7. no saving of lioness networks

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Commits on Jul 20, 2022

  1. no saving of lioness networks

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  2. update lioness test

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  3. lower sizeof test

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  4. update test data

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  7. Merge remote-tracking branch 'upstream/devel'

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  9. reduce panda tests

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Commits on Jul 21, 2022

  1. Update main.yml

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Commits on Aug 16, 2022

  1. 1.1.16 

    update pandapy with header argument (#260)
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Commits on Aug 23, 2022

  1. trying collapse readme (#261) 

    * trying collapse readme

* collapse animal description
    @marouenbg
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  2. Update README.md

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Commits on Oct 31, 2022

  1. Fix news file formatting 

      o was not rendering list properly
    @lshep
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Commits on Nov 1, 2022

  1. bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

    @jwokaty
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  2. bump x.y.z version to odd y following creation of RELEASE_3_16 branch

    @jwokaty
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Commits on Nov 25, 2022

  1. update biconda (#265)

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Commits on Dec 15, 2022

  1. add spider (#269) 

    * add spider

* udpate spider

* udpate spider

* update spuder with degreeadjust

* fix spider bug
    @marouenbg
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Commits on Dec 19, 2022

  1. Merge branch 'master' into devel

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  3. adding spider

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Commits on Dec 21, 2022

  1. DRAGON and unit tests work in progress (#267) 

    - add DRAGON in R and unit tests
    @katehoffshutta
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Commits on Jan 10, 2023

  1. update lioness (#276)

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Commits on Jan 17, 2023

  1. update lioness code (#277)

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  2. Update LIONESS.R

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  3. Update LIONESS.R

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  1. Update LIONESS.R

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Commits on Feb 10, 2023

  1. add note about the function (#279) 

    * add note about the function

* Update sourcePPI.R
    @marouenbg
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Commits on Feb 13, 2023

  1. Update README.md

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  2. Update README.md

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Commits on Feb 15, 2023

  1. Update sourcePPI.R

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  2. Update sourcePPI.R

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  3. add details about sourcePPI (#280)

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Commits on Feb 22, 2023

  1. 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>
    @laurenhsu1 @marouenbg @katehoffshutta
    4 people authored Feb 22, 2023
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Commits on Mar 14, 2023

  1. fix monster error

    @marouenbg
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  2. fix monster

    @marouenbg
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  3. Merge branch 'devel' of git.bioconductor.org:packages/netZooR into devel

    @marouenbg
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  4. 1.3.2

    @marouenbg
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  5. update tests

    @marouenbg
    marouenbg committed Mar 14, 2023
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  6. update bioc verssion

    @marouenbg
    marouenbg committed Mar 14, 2023
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Commits on Mar 16, 2023

  1. update monster test

    @marouenbg
    marouenbg committed Mar 16, 2023
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  2. update argument description

    @marouenbg
    marouenbg committed Mar 16, 2023
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  3. update argument description

    @marouenbg
    marouenbg committed Mar 16, 2023
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  4. changed date

    @marouenbg
    marouenbg committed Mar 16, 2023
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Commits on Mar 19, 2023

  1. updaate docs

    @marouenbg
    marouenbg committed Mar 19, 2023
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Commits on Mar 20, 2023

  1. update dragon verbose

    @marouenbg
    marouenbg committed Mar 20, 2023
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Commits on Mar 21, 2023

  1. update spider

    @marouenbg
    marouenbg committed Mar 21, 2023
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Commits on Mar 22, 2023

  1. prepare for puma

    @marouenbg
    marouenbg committed Mar 22, 2023
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Commits on Apr 12, 2023

  1. add puma (#270) 

    * add puma

* update PUMA

* updating mirna interactions

* add PUMA in readme

* Update PUMA.R
    @marouenbg
    marouenbg authored Apr 12, 2023
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  2. Merge branch 'master' into devel

    @marouenbg
    marouenbg authored Apr 12, 2023
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Commits on Apr 29, 2023

  1. Create TIGER.R (#272) 

    add TIGER.R
    @cchen22
    cchen22 authored Apr 29, 2023
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Commits on May 30, 2023

  1. 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
    @marouenbg
    marouenbg authored May 30, 2023
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Commits on May 31, 2023

  1. 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
    @marouenbg
    marouenbg authored May 31, 2023
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  2. 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>
    @cchen22 @marouenbg
    cchen22 and marouenbg authored May 31, 2023
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Commits on Jun 2, 2023

  1. Update DESCRIPTION

    @marouenbg
    marouenbg authored Jun 2, 2023
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  2. 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>
    @cchen22 @marouenbg
    cchen22 and marouenbg authored Jun 2, 2023
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  3. Merge branch 'master' into devel

    @marouenbg
    marouenbg authored Jun 2, 2023
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Commits on Sep 2, 2023

  1. 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>
    @soelmicheletti @marouenbg
    @nturaga @katehoffshutta @lshep @jwokaty @laurenhsu1 @cchen22
    9 people authored Sep 2, 2023
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Commits on Sep 7, 2023

  1. Update README.md

    @marouenbg
    marouenbg authored Sep 7, 2023
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Commits on Sep 18, 2023

  1. Update TIGER (#297)

    @cchen22
    cchen22 authored Sep 18, 2023
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  2. 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>
    @soelmicheletti @marouenbg
    @nturaga @katehoffshutta @lshep @jwokaty @laurenhsu1 @cchen22
    9 people authored Sep 18, 2023
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Commits on Sep 25, 2023

  1. 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
    @marouenbg
    marouenbg authored Sep 25, 2023
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Commits on Nov 3, 2023

  1. Update README.md

    @marouenbg
    marouenbg authored Nov 3, 2023
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  2. Update main.yml

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  3. Update main.yml

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  4. Update main.yml

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Commits on Nov 9, 2023

  1. Fixed dependency on uchardet (#301) 

    * Fixed dependency on uchardet

* Removed RCy3 from Imports

* Added RCy3 back to Imports
    @taraeicher
    taraeicher authored Nov 9, 2023
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  2. 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>
    @soelmicheletti @marouenbg
    soelmicheletti and marouenbg authored Nov 9, 2023
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Commits on Nov 18, 2023

  1. Merge branch 'master' into devel

    @marouenbg
    marouenbg authored Nov 18, 2023
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  2. Update README.md

    @marouenbg
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Commits on Dec 1, 2023

  1. 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
    @katehoffshutta
    katehoffshutta authored Dec 1, 2023
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Commits on Feb 3, 2024

  1. 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
    @marouenbg
    marouenbg authored Feb 3, 2024
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Commits on Feb 17, 2024

  1. Update README.md

    @marouenbg
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Commits on Mar 3, 2024

  1. 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
    @marouenbg
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Commits on Mar 4, 2024

  1. 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
    @marouenbg
    marouenbg authored Mar 4, 2024
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Commits on Mar 8, 2024

  1. merged 1.5.17

    @marouenbg
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Commits on Jun 24, 2024

  1. Update main.yml

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  2. Update main.yml

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  3. Update main.yml

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  4. Update main.yml

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Commits on Jun 28, 2024

  1. 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
    @taraeicher
    taraeicher authored Jun 28, 2024
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Commits on Jul 23, 2024

  1. 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
    @taraeicher
    taraeicher authored Jul 23, 2024
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  2. Merge branch 'master' into devel

    @marouenbg
    marouenbg authored Jul 23, 2024
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