0a9d044 (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 10:52:14 -0400;
449b0a6 (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 10:52:14 -0400;
445be20 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 10:49:02 -0400;
8141450 (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 10:49:02 -0400;
793625e vignette errors by
Jermiah <jermiahjoseph@gmail.com>2023-04-21 17:57:37 +0000;
bff0ca3 vignette errors by
Jermiah <jermiahjoseph@gmail.com>2023-04-21 17:40:02 +0000;
2b60c5a fixing function issues by
Jermiah <jermiahjoseph@gmail.com>2023-04-21 17:12:44 +0000;
6bbbb8a github dependencies error test by
Jermiah <jermiahjoseph@gmail.com>2023-04-20 17:05:28 +0000;
cc98d4e github dependencies error test by
Jermiah <jermiahjoseph@gmail.com>2023-04-20 17:05:23 +0000;
da3ec0b added windows and mac GHA by
Jermiah <jermiahjoseph@gmail.com>2023-04-20 15:23:04 +0000;
46abfb0 fixed date by
Jermiah <jermiahjoseph@gmail.com>2023-04-19 20:46:45 +0000;
390b966 Bumped version number by
Jermiah <jermiahjoseph@gmail.com>2023-04-19 18:21:46 +0000;
eb4e850 fixing logLogistic Fxn by
Jermiah <jermiahjoseph@gmail.com>2023-04-19 17:23:00 +0000;
1e7ffc7 fixed typo. added molecularprofiles to cset. fixed dataset(s) typo by
Jermiah BHK <jermiahjoseph98@gmail.com>2023-03-08 20:29:58 -0500;
e90c241 Version bump for Bioc push by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-12 18:11:42 -0500;
eae211c Debugging vignette issues on Bioconductor by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-12 17:16:53 -0500;
6cf09a1 Moved vignette data to inst to fix missing file error on Bioconductor; updated .Rbuildignore to allow .tar.gz files by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-12 16:25:30 -0500;
faa09eb Fix merge conflicts with upstream by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-07 10:34:55 -0500;
385f46b Version bump for Bioc push by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-07 10:33:12 -0500;
21e632e Merge pull request <a href="#132">#132</a> from bhklab/development by
Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>2022-12-06 21:36:36 -0500;
fdd3ab0 Add R.utils to suggests to allow reading compressed csv files in new drug combination vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-06 18:46:41 -0500;
0f9da06 Fix R and Bioconductor versions in GHA by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-06 18:38:23 -0500;
aba4520 Fix r-lib/actions branch in GHA by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-06 18:33:28 -0500;
14aede5 Fix branch name for r-lib/actions in GHA by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-06 18:29:11 -0500;
921874f Finalized edits for drug synergy vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-06 18:23:14 -0500;
c83bdae Finished first pass proof read by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-06 17:39:07 -0500;
7a70c17 Finished all vignette text, knitting to proof read by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-06 16:34:51 -0500;
14e30e1 Finalizing text for drug combination vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-12-06 14:59:50 -0500;
54fda64 Completing monotherapy curve fit section of drug combo vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-28 18:10:12 -0500;
dc303c4 Finished TRE creation section of vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-28 12:59:13 -0500;
e678260 Fix missing values and cleaned up drug synergy visualization by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-28 12:29:39 -0500;
bae83b0 Add description of Mathews Griner dataset to drug combos vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-28 10:32:22 -0500;
c6fb2bd Add bibliography for drug combinations vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-25 15:33:28 -0500;
347ceb0 Clustering by actual or predicted viability partitions curves into broader response patterns by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-03 19:09:56 -0400;
b749f6e Clustering monotherapy curves to look for bad fit trends * Also cleaned up some code formatting in filterNoisyCurves.R by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-03 13:46:09 -0400;
f7e96c7 Adding plots to determine appropriate Rsquared filter to get better agreement between synergy metrics by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-02 18:51:56 -0400;
e139ca7 Update remote by
Christopher Eeles <christopher.eeles@outlook.com>2022-11-01 17:13:31 -0400;
f879f2d 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 11:14:17 -0400;
58af756 (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 11:14:17 -0400;
6833673 Add header to distinguish 2 from jump to 3 by
lshep <lori.shepherd@roswellpark.org>2022-10-31 13:59:22 -0400;
e9a139e Add ZIP delta calculation to vignette, but results seem wrong; need to audit the code by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-27 19:11:44 -0400;
753fbf8 Fix names of returned arguments in estimateProjParams such that EC50 and E_inf are assigned to the correct columns by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-27 18:00:59 -0400;
cfb3d1c Fix bug in estimteProjParams where E)inf was being unlogged instead of EC50 by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-27 17:46:33 -0400;
d5cb925 Fix bug is estimateProjParams caused by passing lower_bounds as upper_bounds in .fitCurve2 call by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-27 17:18:32 -0400;
5f05d41 Fix bug in estimateProjParams caused by dropping zero concentration in .reformatData by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-27 16:08:23 -0400;
2ef3520 Computed synergy Null references for Mathews Griner vignette by
ChristopherEeles <christopher.eeles@outlook.com>2022-10-26 15:58:35 -0400;
83402cd Preparing to compute synergy metrics in Mathews Griner vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-25 19:39:51 -0400;
6af5b20 Fitting monotherapy curves for Mathews Griner dataset vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-25 17:45:51 -0400;
1279287 Add basic template for drug combo vignette by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-24 13:51:28 -0400;
4570a1d Set R_BIOC_VERSION environment variable in GHA by
Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>2022-10-14 15:27:10 -0400;
08db5ab Version bump for BioC push by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-14 15:06:38 -0400;
db3f092 Merge pull request <a href="#129">#129</a> from bhklab/development by
Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>2022-10-14 15:05:01 -0400;
143e246 Merge branch 'master' into development by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-14 13:34:47 -0400;
b0e96ec Merge pull request <a href="#128">#128</a> from bhklab/test_synergy by
Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>2022-10-14 13:34:01 -0400;
82dc356 Minor refactor and clean up of estimateProjParams logic by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-14 13:27:15 -0400;
8fbc365 Remove commented out old implementation of .fitProjParmsLoss by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-14 13:19:44 -0400;
7ffe773 Remove import by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-14 13:18:41 -0400;
29d0485 Change tabs to spaces in computeSynergy by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-14 13:18:00 -0400;
6ba945a Finally fixed typo in partialCorQUICKSTOP by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-14 13:17:08 -0400;
d61025b Use do.call to avoid repeated code by
ff98li <li.feifei.official@gmail.com>2022-10-13 21:59:08 +0000;
251926b ZIP curve fitting function API changed to fit .fitCurve2 by
ff98li <li.feifei.official@gmail.com>2022-10-12 18:39:05 +0000;
ae8a268 Version bump for Bioc push by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 17:41:36 -0400;
5868865 Allow package cache now that pkgdown deployment worked by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 17:29:22 -0400;
c6e0cf7 Set R_BIOC_VERSION environemtn variable to stop installing ancient CoreGx by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 17:02:33 -0400;
96d66c9 Fix merge conflict by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 16:51:57 -0400;
638a36e Update pkgdown R version by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 16:51:31 -0400;
5c94107 Set R version in pkgdown build by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 16:49:28 -0400;
542290a Merge pull request <a href="#127">#127</a> from bhklab/development by
Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>2022-10-06 16:36:21 -0400;
1e6f605 Fix unresolved merge conflict in computeSynergy by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 16:17:46 -0400;
cf82904 Debugging pkgdown GHA by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 16:04:15 -0400;
eff0774 Merge branch 'development' of github.com:bhklab/PharmacoGx into development by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 13:29:34 -0400;
132e30c Merge LICENSE changes by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 13:29:26 -0400;
dbeb126 Switch LICENSE to GPLv3 by
Christopher Eeles <christopher.eeles@outlook.com>2022-10-06 12:55:31 -0400;
a8cdd1f Merge lastest change of development branch into test_synergy by
ff98li <li.feifei.official@gmail.com>2022-08-29 17:55:31 +0000;
6b62738 Fixed bugs in .deltaScore; projected E_inf added for new arguments by
ff98li <li.feifei.official@gmail.com>2022-08-15 04:46:51 +0000;
85225b3 Add pkgdown GHA workflow by
Christopher Eeles <christopher.eeles@outlook.com>2022-08-10 18:39:32 -0400;
e65c886 Add pkgdown site by
Christopher Eeles <christopher.eeles@outlook.com>2022-08-10 18:38:54 -0400;
1876e5d Merge branch 'development' of https://github.com/bhklab/PharmacoGx into test_synergy by
ff98li <li.feifei.official@gmail.com>2022-07-27 20:24:05 +0000;
791b849 Renamed hill4Par to hillCurve, updated documentation and set default E_ninf=1 by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-26 14:55:36 -0400;
6e2369c Merge branch 'master' into development by
ChristopherEeles <christopher.eeles@outlook.com>2022-07-25 17:06:08 -0400;
4ccd3cb Updated .computeZIPdelta API design and documentaion by
ff98li <li.feifei.official@gmail.com>2022-07-25 16:22:00 +0000;
1803174 Added drc back in this branch for testing by
ff98li <li.feifei.official@gmail.com>2022-07-24 05:38:32 +0000;
39be514 Removed drc. The commit before the last one was resolving merge conflict. by
ff98li <li.feifei.official@gmail.com>2022-07-24 05:31:18 +0000;
59671ab Updated synergy functions to be compatible with combo_viability renamed from viability. Updated function examples. Extra argument show_Rsqr added for computeZIPdelta. by
ff98li <li.feifei.official@gmail.com>2022-07-24 05:07:14 +0000;
fc83502 Updated synergy functions to be compatible with combo_viability renamed from viability. Updated function examples. Extra argument show_Rsqr added for computeZIPdelta. by
ff98li <li.feifei.official@gmail.com>2022-07-24 05:06:53 +0000;
a9825ba Version bump for BioC push by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-21 20:39:11 -0400;
f79a830 Merge pull request <a href="#126">#126</a> from bhklab/development by
Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>2022-07-21 20:34:51 -0400;
25a255d Renamed a few more synergy function to match BioC best practices; fix package NAMESPACE after renaming by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-21 20:13:56 -0400;
b0bada8 Fix outdated example in hill_4par; renamed function to follow BioC best practices by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-21 20:01:32 -0400;
a054901 Update man files after merge PR <a href="#125">#125</a> by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-21 15:05:09 -0400;
f263b1f Merge pull request <a href="#125">#125</a> from bhklab/test_synergy by
Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>2022-07-21 14:58:59 -0400;
49fcf2f Fix merge conflict with development by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-21 14:55:57 -0400;
775bc77 Refactored computeZIPDelta to allow reusing pre-computed ZIP values by
ff98li <li.feifei.official@gmail.com>2022-07-21 01:38:46 +0000;
b355c15 Replaced projViability with Hill_4par to allow for 4-parameter fitting. Added plotting function to plot projected Hill curves. Fixed bugs in using .fitCurve. Replaced L2-loss with log-cosh loss. by
ff98li <li.feifei.official@gmail.com>2022-07-20 21:09:21 +0000;
af0a751 Created new branch by
ff98li <li.feifei.official@gmail.com>2022-07-15 21:51:54 +0000;
28e9056 Increment version number for BioC push; update NEWS.md by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-13 13:07:03 -0400;
df8f04b Merge pull request <a href="#123">#123</a> from bhklab/development by
Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>2022-07-13 13:00:18 -0400;
7ddda3a Add examples to computeSynergy functions to correct error in BiocCheck by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-13 12:42:24 -0400;
a581ec3 Fix downloadPSet to resave the data after calling updateObject internally by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-13 12:02:13 -0400;
a5bdb23 Merge branch 'development' of github.com:bhklab/PharmacoGx into development by
Christopher Eeles <christopher.eeles@outlook.com>2022-07-12 18:12:23 -0400;
