Fixed dependency on uchardet #301
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## devel #301 +/- ##
=======================================
Coverage 40.76% 40.76%
=======================================
Files 23 23
Lines 2838 2838
=======================================
Hits 1157 1157
Misses 1681 1681 ☔ View full report in Codecov by Sentry. |
marouenbg
added a commit
that referenced
this pull request
Nov 26, 2023
* add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Added COBRA method (#293) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Update README.md * Update TIGER (#297) * Smaller changes in COBRA (#296) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method * Exported COBRA and improved description --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Cobra docs (#298) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add cobra docs * build new website * update package * update package * add package * export pandaR classes * add site html * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * Update README.md * Update main.yml * Update main.yml * Update main.yml * Fixed dependency on uchardet (#301) * Fixed dependency on uchardet * Removed RCy3 from Imports * Added RCy3 back to Imports * Feature: included pcor decomposition natively in cobra (#299) * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Update COBRA.R --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update README.md --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> Co-authored-by: Soel Micheletti <soel.micheletti@hotmail.it> Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
marouenbg
added a commit
that referenced
this pull request
Mar 8, 2024
* add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Added COBRA method (#293) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Update README.md * Update TIGER (#297) * Smaller changes in COBRA (#296) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method * Exported COBRA and improved description --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Cobra docs (#298) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add cobra docs * build new website * update package * update package * add package * export pandaR classes * add site html * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * Update README.md * Update main.yml * Update main.yml * Update main.yml * Fixed dependency on uchardet (#301) * Fixed dependency on uchardet * Removed RCy3 from Imports * Added RCy3 back to Imports * Feature: included pcor decomposition natively in cobra (#299) * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Update COBRA.R --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update README.md * Fix dragon (#306) * add DRAGON outline * implemented vars and esqs, added tests * added optim * Added fn to get shrunken cov and unit tests * Update DESCRIPTION * Update DESCRIPTION * mechanics for prec mat and parcor * added testdata directory * fixed test paths * Update test-dragon.R * added export function and tests * updated docs * added ex datasets * fixed bug w/self-edges in GGM * fixed GGM diagonal issue * fixed merge conflicts in docs * fixed more merge conflicts * Fix 309 (#310) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix 309 * Update README.md * Aadd yarn (#314) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add yarn * add yarn * add yarn * change yarn vignette * change yarn vignette * change yarn vignette * add download data set * add download data set * update yarn * update yarn * update yarn * update yarn * add download file * add download file * add download file * update workflow * update workflow * update to R 4.3 * update to R 4.3 * Add monster desc (#312) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add monster description --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> Co-authored-by: Soel Micheletti <soel.micheletti@hotmail.it> Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
marouenbg
added a commit
that referenced
this pull request
Jun 8, 2024
* add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Added COBRA method (#293) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Update README.md * Update TIGER (#297) * Smaller changes in COBRA (#296) * 1.4.0 (#289) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * Fix news file formatting o was not rendering list properly * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug * DRAGON and unit tests work in progress (#267) - add DRAGON in R and unit tests * update lioness (#276) * update lioness code (#277) * Update LIONESS.R * Update LIONESS.R * Update LIONESS.R * add note about the function (#279) * add note about the function * Update sourcePPI.R * Update README.md * Update README.md * Update sourcePPI.R * Update sourcePPI.R * add details about sourcePPI (#280) * add parallelization option to lioness (#281) * 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * fix monster error * fix monster * 1.3.2 * update tests * update bioc verssion * update monster test * update argument description * update argument description * changed date * updaate docs * update dragon verbose * update spider * add puma (#270) * add puma * update PUMA * updating mirna interactions * add PUMA in readme * Update PUMA.R * Create TIGER.R (#272) add TIGER.R * Add lioness update (#284) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code * Update puma (#286) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix puma examples * fix puma examples * update docs * Add TIGER (#283) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update DESCRIPTION * Add TIGER description to README file (#288) * Create TIGER.R add TIGER.R * Add TIGER * compile TIGER 1. change the TIGER example to fit LazyData=F mode 2. document all the functions and required packages * DESCRIPTION depends Add cmdstanr to DESCRIPTION depends * onLoad install cmdstan * Update puma.Rd * Add data document * Update README.md --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Added COBRA method * Exported COBRA and improved description --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> * Cobra docs (#298) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add cobra docs * build new website * update package * update package * add package * export pandaR classes * add site html * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * Update README.md * Update main.yml * Update main.yml * Update main.yml * Fixed dependency on uchardet (#301) * Fixed dependency on uchardet * Removed RCy3 from Imports * Added RCy3 back to Imports * Feature: included pcor decomposition natively in cobra (#299) * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Feature: included pcor decomposition natively in cobra * Update COBRA.R --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> * Update README.md * Fix dragon (#306) * add DRAGON outline * implemented vars and esqs, added tests * added optim * Added fn to get shrunken cov and unit tests * Update DESCRIPTION * Update DESCRIPTION * mechanics for prec mat and parcor * added testdata directory * fixed test paths * Update test-dragon.R * added export function and tests * updated docs * added ex datasets * fixed bug w/self-edges in GGM * fixed GGM diagonal issue * fixed merge conflicts in docs * fixed more merge conflicts * Fix 309 (#310) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * fix 309 * Update README.md * Aadd yarn (#314) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add yarn * add yarn * add yarn * change yarn vignette * change yarn vignette * change yarn vignette * add download data set * add download data set * update yarn * update yarn * update yarn * update yarn * add download file * add download file * add download file * update workflow * update workflow * update to R 4.3 * update to R 4.3 * Add monster desc (#312) * update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add monster description --------- Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> Co-authored-by: lshep <lori.shepherd@roswellpark.org> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com> Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com> Co-authored-by: Soel Micheletti <soel.micheletti@hotmail.it> Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Bioconductor version of imported package RCy3 depends on defunct package uchardet. Fixed this by switching to the dev version of RCy3 (GitHub repo cytoscape/RCy3).