1. CoreGx
  2. Graph
Graph of CoreGx
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  • 143debb (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 11:22:13 -0400;
  • ba1a202 (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 11:22:13 -0400;
  • 2a65312 modified LongTable class to allowCartesian by Jermiah <jermiahjoseph@gmail.com> 2023-09-29 20:14:29 +0000;
  • 1b5d4a8 bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 11:18:08 -0400;
  • 788cc40 (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 11:18:08 -0400;
  • 9e809f8 Bioc Push by Jermiah <jermiahjoseph@gmail.com> 2023-04-20 17:08:45 +0000;
  • 29d7457 version bump and date by Jermiah <jermiahjoseph@gmail.com> 2023-04-20 15:42:03 +0000;
  • 52a3259 added macOS and windows GHA by Jermiah <jermiahjoseph@gmail.com> 2023-04-20 00:56:06 +0000;
  • a057193 fixing warnings by Jermiah <jermiahjoseph@gmail.com> 2023-04-19 22:21:25 +0000;
  • 2e89257 fixed generic S3 function error by Jermiah <jermiahjoseph@gmail.com> 2023-04-19 18:11:17 +0000;
  • 647bdc8 Address error in optimization functions by Jermiah <jermiahjoseph@gmail.com> 2023-04-19 17:33:03 +0000;
  • 5299b01 fixed warning in as.data.table s3 function by Jermiah <jermiahjoseph@gmail.com> 2023-04-18 21:03:10 +0000;
  • d35bb2f added return line that was previously removed by Jermiah BHK <jermiahjoseph98@gmail.com> 2023-03-06 16:01:51 -0500;
  • 4cb1d99 Fix bug in .checkForIdColumn and increment version for BioC push by Christopher Eeles <christopher.eeles@outlook.com> 2023-03-02 19:54:34 -0500;
  • 2f4f4d7 Fix errors on BioC caused by clevelandSmall_cSet being really old by Christopher Eeles <christopher.eeles@outlook.com> 2023-02-18 16:38:44 -0500;
  • dbcb58d Version bump for Bioc push by Christopher Eeles <christopher.eeles@outlook.com> 2022-12-12 18:09:52 -0500;
  • da50922 Merge pull request <a href="#167">#167</a> from bhklab/development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-12-12 12:39:28 -0500;
  • ce78101 Merge branch 'main' into development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-12-12 12:25:44 -0500;
  • a4f75cf Add manual pages before PR by Christopher Eeles <christopher.eeles@outlook.com> 2022-12-12 17:24:18 -0500;
  • d4c4df8 Fix bug in assays,TreatmentResponseExperiment causing warning when trying to delete no columns by Christopher Eeles <christopher.eeles@outlook.com> 2022-12-12 16:53:26 -0500;
  • 26ad6fb Fix GHA names to reflect release vs development CI/CD jobs by Christopher Eeles <christopher.eeles@outlook.com> 2022-12-06 18:44:01 -0500;
  • a13f1c0 Fix GHA workflows by Christopher Eeles <christopher.eeles@outlook.com> 2022-12-06 18:42:10 -0500;
  • f50e968 Fix R version, Bioconductor version and r-lib/actions branch in GHA by Christopher Eeles <christopher.eeles@outlook.com> 2022-12-06 18:41:36 -0500;
  • d5b1bec Fix aggregate2 by Christopher Eeles <christopher.eeles@outlook.com> 2022-11-28 16:59:26 -0500;
  • b2057ff Merge branch 'master' by Christopher Eeles <christopher.eeles@outlook.com> 2022-11-28 15:53:34 -0500;
  • 0f3b984 bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:22:04 -0400;
  • 681e43d (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:22:04 -0400;
  • 7782a39 Fix news formatting by lshep <lori.shepherd@roswellpark.org> 2022-10-31 13:27:57 -0400;
  • 13fad56 Updating closure environment in drop_fn_params as well as rebyte compiling by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-27 16:23:30 -0400;
  • e5fb6bd Merge branch 'development' by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-13 17:38:04 -0400;
  • 01aa9a4 Version bump for BioC push by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-13 17:36:34 -0400;
  • b0c6c24 Merge pull request <a href="#165">#165</a> from bhklab/development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-10-13 17:20:32 -0400;
  • 56bf9a9 Removed first positional argument name from .fitCurve to fix downstream bug in RadioGx due to different argument names by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-13 15:13:25 -0400;
  • 9610d20 Add GPLv3 license file by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-06 12:42:22 -0400;
  • 16eae9f Merge pull request <a href="#164">#164</a> from bhklab/development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-10-04 18:33:32 -0400;
  • 1051af8 Fix documentation to pass checks by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-04 18:18:06 -0400;
  • 959cc22 Cleaned up documentation to fix check errors/warnings by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-04 17:51:51 -0400;
  • ec3e821 Fix incorrect testing package name in test-utils-optimization.R by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-04 16:54:25 -0400;
  • de6946f Regenerate NAMESPACE and man by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-04 16:36:51 -0400;
  • e367955 Remove make_optim_loss helper by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-04 16:34:20 -0400;
  • 0709d2f Pre-merge with master by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-04 16:09:08 -0400;
  • 716d5b9 Add optim_only option to .fitCurve2 by Christopher Eeles <christopher.eeles@outlook.com> 2022-10-03 16:38:14 -0400;
  • f34b615 Modified fitCurve tests to run within a reasonable time frame by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-30 19:07:10 -0400;
  • 7bf693d Add usage example to .fitCurve2 by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-30 17:40:59 -0400;
  • aafa8a5 Added tests for .fitCurve and .fitCurve2; tests passing by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-30 17:07:30 -0400;
  • 4726ff8 Loss function equivalence tests passing by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-30 15:48:08 -0400;
  • b2697bd Fix bugs in .normal_loss and .cauchy_loss; added unit tests for new loss being equal to .residual by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-30 15:33:54 -0400;
  • a8edc61 .fitCurve2 done, testing vs .fitCurve by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-30 12:45:32 -0400;
  • abd27b9 Add first attempt at .meshEval2 function by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-29 17:01:11 -0400;
  • 0345bfe Add more optim helper methods to reformat general R functions into functions optimizable via stats::optim by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-27 14:37:57 -0400;
  • 08e34ee Add helper methods to fix function parameters and collect parameters into a single list by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-27 13:34:59 -0400;
  • 168029b Merge branch 'development' of github.com:bhklab/CoreGx into development by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-26 16:41:00 -0400;
  • cea9227 Further refactoring .fitCurve2 by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-26 16:40:31 -0400;
  • 002bfd9 Merged with remote update by ff98li <li.feifei.official@gmail.com> 2022-09-23 19:21:41 +0000;
  • eda95f1 buildComboProfiles: Allow to build a drug combo profile without combo_viability in tre by ff98li <li.feifei.official@gmail.com> 2022-09-23 19:18:26 +0000;
  • cbdc842 Add optim method to .fitCurve2 by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-21 21:18:54 -0400;
  • c082779 Refactoring .fitCurve to .fitCurve2 with parameterized loss function by Christopher Eeles <christopher.eeles@outlook.com> 2022-09-21 21:13:48 -0400;
  • 50a30e6 Add pkgdown site GHA by Christopher Eeles <christopher.eeles@outlook.com> 2022-08-10 17:53:48 -0400;
  • 7bac989 Add pkgdown template by Christopher Eeles <christopher.eeles@outlook.com> 2022-08-10 17:52:20 -0400;
  • 58b025f Version bump for BioC push; updated NEWS.md by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-25 15:52:29 -0400;
  • 9f4612d Merge pull request <a href="#163">#163</a> from bhklab/development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-07-25 15:36:44 -0400;
  • 33203de Fix bug when deleting assays with NULL assigned; add names S4-method for LongTable to allow autocomplete via dollar sign access by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-25 15:27:15 -0400;
  • ed91bb5 Updated buildComboProfiles to be compatible with bio_rep and tech_rep and combo_viability by ff98li <li.feifei.official@gmail.com> 2022-07-24 05:10:32 +0000;
  • 06036a5 Merge pull request <a href="#162">#162</a> from bhklab/development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-07-23 15:44:51 -0400;
  • 231325a Merge pull request <a href="#161">#161</a> from bhklab/development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-07-23 15:32:26 -0400;
  • eb5ad22 Update TRE objects embedded in example data; fixed bug in LongTable to data.table coercion failing to attach metadata by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-23 15:31:25 -0400;
  • a0879b9 Tests passing with renamed internal assay keys and new example data; debugging vignette by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-23 14:38:03 -0400;
  • 1de0afe Modified internal assay primary keys to be prepended with a dot to prevent column name clashes by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-23 13:52:39 -0400;
  • 89bd47f Tested assayIndex_rework with NCI_ALMANAC analysis script and everything seems to work fine by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-23 12:17:05 -0400;
  • 352421a All tests passing after assayIndex rework; package works or tests are incomplete? by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-22 21:23:55 -0400;
  • 980f640 Improve test documentation by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-22 21:21:34 -0400;
  • b9fc546 Testing removal of all NA assayIndex rows by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-22 21:19:10 -0400;
  • 3a55565 Merge branch 'development' into assayIndex_rework by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-22 20:25:01 -0400;
  • 660d0b9 Clarified subset,LongTable-method documentation; Fixes <a href="#160">#160</a> by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-22 20:20:17 -0400;
  • 9ed9cb7 End of day push by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-22 18:01:16 -0400;
  • 9d2adf9 Removing rows with all NA index values in assayIndex to fix memory usage issues by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-22 13:35:22 -0400;
  • ae36175 Version bump for BioC push by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-21 19:37:50 -0400;
  • 7bbc8d5 Merge pull request <a href="#159">#159</a> from bhklab/development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-07-21 19:30:17 -0400;
  • b787bb1 Fix merge conflicts with main by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-21 19:07:42 -0400;
  • 0341840 Fix ##158 by string wrapping assays when there are too many to fit on one line by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-21 19:03:44 -0400;
  • 154aa9a Remove i from method signature of assay<- and handle type checking inside of method by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-21 17:01:43 -0400;
  • eb88d28 Fix bug in assay method causing information loss when assigning a table with existing key; Fix <a href="#153">#153</a> so NULL now deleted an assay by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-21 16:57:52 -0400;
  • 0503c28 Remove testing code from CoreGx R files by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-21 12:16:53 -0400;
  • 7d6bd4e Merge branch 'development' of github.com:bhklab/CoreGx into development by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-21 12:07:29 -0400;
  • 58568f1 Fix bug in aggregate2 where splitting the data for parallelization didn't split into nthread objects by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-21 12:07:24 -0400;
  • 53fb6ef Resolved all TODOs and fixed bugs in buildComboProfiles. Enabled option to exclude viability without removing the column after calculating it. by ff98li <li.feifei.official@gmail.com> 2022-07-20 21:02:00 +0000;
  • f0bf2fd Update aggregate2 documentation to reflect changes in parallelization strategy by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-18 14:07:45 -0400;
  • 10c300e Updated parallelization strategy for aggregate2 * Function now splits into one table per thread instead of one table per group * Should reduce memory usage and ensure that parallelization is always faster than serial data.table aggregates (which was not the case previously) by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-18 13:37:50 -0400;
  • 3d7b408 Merge with upstream by ChristopherEeles <christopher.eeles@outlook.com> 2022-07-18 13:35:31 -0400;
  • 37647ed Fix failing unit tests; increment package cache for GHA workflow by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-12 21:38:18 -0400;
  • b7c6858 Merge with upstream main; updated package date; update NEWS.md by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-12 19:01:45 -0400;
  • 210aa34 Remove testing code and increment version number for BioC push by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-12 18:59:03 -0400;
  • b7444dc Add call.=FALSE in warning calls inside aggregate,LongTable-method by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-12 18:57:35 -0400;
  • bb9e787 Merge pull request <a href="#157">#157</a> from bhklab/development by Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com> 2022-07-12 18:56:51 -0400;
  • eeef305 Fix typo in assay,LongTable-method causing Rcmdcheck to fail by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-12 18:37:59 -0400;
  • efc881b Add useful error message to show,CoreSet-method when updateObject needs to be used on outdated class structure by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-12 18:13:24 -0400;
  • 9135185 Merge branch 'development' of github.com:bhklab/CoreGx into development by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-11 16:51:48 -0400;
  • d8994d1 Add moreArgs argument to aggregate2, aggregate and endoaggregate to allow passing non-column arguments by Christopher Eeles <christopher.eeles@outlook.com> 2022-07-11 16:51:45 -0400;
  • 0ed63b2 Updated to S4 by ff98li <li.feifei.official@gmail.com> 2022-07-09 02:07:53 +0000;
  • e183fa9 util method for joining drug combo profiles from any TRE assays added. commented failing tests. by ff98li <li.feifei.official@gmail.com> 2022-07-05 18:51:01 +0000;