Bioconductor Code: edgeR

Graph of edgeR

3b722704 (origin/RELEASE_3_18, RELEASE_3_18) edgeR 4.0.2 - catchSalmon() now detects whether resamples are Gibbs or bootstrap. - catchSalmon and catchKallisto help page now explains columns of `annotation` output. by Gordon Smyth <smyth@wehi.edu.au> 2023-11-19 09:48:35 +1100;
483a293d (HEAD -> devel, origin/master, origin/devel, origin/HEAD) edgeR 4.1.2 - catchSalmon() now detects whether resamples are Gibbs or bootstrap. - catchSalmon and catchKallisto help page now explains columns of `annotation` output. by Gordon Smyth <smyth@wehi.edu.au> 2023-11-19 07:50:42 +1100;
4e233eb6 Fix typo. by Gordon Smyth <smyth@wehi.edu.au> 2023-10-30 21:39:00 +1100;
df0d93b4 Fix typo. by Gordon Smyth <smyth@wehi.edu.au> 2023-10-30 21:38:35 +1100;
dfc4d79d Fix typo. by Gordon Smyth <smyth@wehi.edu.au> 2023-10-30 21:36:35 +1100;
d236d345 Undeprecate decidetestsDGE(). The deprecation is only in the developmental repository. by Gordon Smyth <smyth@wehi.edu.au> 2023-10-29 12:29:52 +1100;
8e4c7fb7 edgeR 4.0.1 - Deprecate decideTestsDGE in favor of decideTests. - Add more detail to decideTests.GLMLRT documentation about logFC cutoffs. by Gordon Smyth <smyth@wehi.edu.au> 2023-10-29 12:11:40 +1100;
af41fc2c More edits to decidetestsDGE.Rd by Gordon Smyth <smyth@wehi.edu.au> 2023-10-29 12:10:36 +1100;
8474362a edgeR 4.1.1 - Deprecate decideTestsDGE in favor of decideTests. - Add more detail to decideTests.GLMLRT documentation about logFC cutoffs. by Gordon Smyth <smyth@wehi.edu.au> 2023-10-29 11:09:46 +1100;
ec4f0d12 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 09:40:33 -0400;
521264a9 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 09:40:33 -0400;
7a0810d6 edgeR 3.99.6 - Update subsetting.R for objects created by new glmQLFit method with legacy=FALSE by Gordon Smyth <smyth@wehi.edu.au> 2023-10-21 12:47:50 +1100;
13d3fc11 edgeR 3.99.5 - Remove working.dispersion as output from glmQLFit and replace with average.ql.dispersion - Revise glmQLFit.Rd by Gordon Smyth <smyth@wehi.edu.au> 2023-10-19 22:39:07 +1100;
041d8948 Revise NEWS.Rd by Gordon Smyth <smyth@wehi.edu.au> 2023-10-18 20:40:23 +1100;
948ccbd6 Split long usage lines by Gordon Smyth <smyth@wehi.edu.au> 2023-10-18 20:35:08 +1100;
f1d8522f Update edgeR user's guide. by Yunshun Chen <yuchen@wehi.edu.au> 2023-10-18 15:41:48 +1100;
3e7ecddf Merge branch 'devel' of git.bioconductor.org:packages/edgeR into devel by Yunshun Chen <yuchen@wehi.edu.au> 2023-10-18 15:40:43 +1100;
e24d4661 edgeR 3.99.4 - Bug fix to glmQLFit (fit$deviance instead of fit$deviances) by Gordon Smyth <smyth@wehi.edu.au> 2023-10-18 15:21:15 +1100;
8eef996c Merge branch 'devel' of git.bioconductor.org:packages/edgeR into devel by Yunshun Chen <yuchen@wehi.edu.au> 2023-10-18 15:13:49 +1100;
2a59afc3 Bug fixing and minor edits to glmQLFit(). by Yunshun Chen <yuchen@wehi.edu.au> 2023-10-18 15:13:12 +1100;
cae4f0ab Update Baldoni et al (2023) reference by Gordon Smyth <smyth@wehi.edu.au> 2023-10-17 21:40:43 +1100;
bee75e76 Bug fixing to geneset-DGEGLM.R by Yunshun Chen <yuchen@wehi.edu.au> 2023-10-16 16:14:29 +1100;
16dbb399 Added documentations to gene set test functions (S3 method for DGEGLM object). by Yunshun Chen <yuchen@wehi.edu.au> 2023-10-16 15:15:50 +1100;
cb878bad Bug fixing to .zscoreGLM() by Yunshun Chen <yuchen@wehi.edu.au> 2023-10-16 13:11:19 +1100;
8faab9e9 edgeR 3.99.3 - Update all the changes to align with the local github by Yunshun Chen <yuchen@wehi.edu.au> 2023-10-16 10:22:46 +1100;
6b8a9fcc edgeR 3.99.2 - Fix voomLmFit() bug when sample weights are set as prior.weights. by Gordon Smyth <smyth@wehi.edu.au> 2023-10-14 22:32:47 +1100;
40d5da8f edgeR 3.99.1 - Edit catchSalmon() help page by Gordon Smyth <smyth@wehi.edu.au> 2023-10-11 15:48:28 +1100;
eca0fbb4 edgeR 3.99 - Lizhong Chen's updates to glmQLFit() including changes to C code. by Gordon Smyth <smyth@wehi.edu.au> 2023-09-26 15:02:40 +1000;
4b1d6892 edgeR 3.43.8 - Remove statmod from suggested packages because limma now imports it by Gordon Smyth <smyth@wehi.edu.au> 2023-08-02 10:03:44 +1000;
a0b0c7e2 Rename edgeR.Rmd to intro.Rmd, no change to resulting vignette. by Gordon Smyth <smyth@wehi.edu.au> 2023-06-21 20:09:59 +1000;
84bd773c edgeR 3.43.7 - Lengthen edgeR.Rmd and change title. by Gordon Smyth <smyth@wehi.edu.au> 2023-06-21 19:59:02 +1000;
57fc32c1 edgeR 3.43.6 - Convert User's Guide to be a formal Vignette with imported pdf. - Delete index.html from inst/doc. by Gordon Smyth <smyth@wehi.edu.au> 2023-06-20 10:55:03 +1000;
035f943b edgeR 3.43.5 - Add BiocStyle to Suggests field of DESCRIPTION. by Gordon Smyth <smyth@wehi.edu.au> 2023-06-19 13:32:14 +1000;
b3b48947 Minor edit to edgeR.Rmd by Gordon Smyth <smyth@wehi.edu.au> 2023-06-10 10:48:53 +1000;
da2084aa edgeR 3.43.4 - Convert vignette from Sweave and pdf to Rmd and html. by Gordon Smyth <smyth@wehi.edu.au> 2023-06-10 10:38:29 +1000;
63d1dc66 (origin/RELEASE_3_17, RELEASE_3_17) edgeR 3.42.4 - Expand Details section of filterByExpr.Rd. by Gordon Smyth <smyth@wehi.edu.au> 2023-05-31 22:47:25 +1000;
0a127fd8 edgeR 3.43.3 - Expand Details section of filterByExpr.Rd by Gordon Smyth <smyth@wehi.edu.au> 2023-05-31 22:42:02 +1000;
9ad0a821 edgeR 3.42.3 - Add statmod to Suggests field of DESCRIPTION file. by Gordon Smyth <smyth@wehi.edu.au> 2023-05-31 09:15:33 +1000;
05723efc edgeR 3.43.2 by Gordon Smyth <smyth@wehi.edu.au> 2023-05-21 11:48:41 +1000;
b0ed0373 Bump version to trigger rebuild and propagation of new Mac binary by J Wokaty <jwokaty@users.noreply.github.com> 2023-05-02 09:47:38 -0400;
182791fe Bump version to trigger rebuild and propagation of new Mac binary by J Wokaty <jwokaty@users.noreply.github.com> 2023-05-01 20:11:38 -0400;
576d8b77 Bump version to trigger rebuild and propagation of new Mac binary by J Wokaty <jwokaty@users.noreply.github.com> 2023-05-01 20:09:55 -0400;
d5d90466 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 09:47:30 -0400;
197b9a8c 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 09:47:30 -0400;
a0193b6d edgeR 3.41.9 - Re-organize NEWS.Rd entries for this release. by Gordon Smyth <smyth@wehi.edu.au> 2023-04-23 22:16:26 +1000;
7a4ce1cb Update NEWS.Rd and the User's guide PDF by Yunshun Chen <yuchen@wehi.edu.au> 2023-04-17 10:56:05 +1000;
7cc2ed00 Update test file by Yunshun Chen <yuchen@wehi.edu.au> 2023-04-12 12:10:06 +1000;
c483076f edgeR 3.41.8 by Gordon Smyth <smyth@wehi.edu.au> 2023-04-11 22:39:33 +1000;
9bc2d102 edgeR 3.41.7 by Gordon Smyth <smyth@wehi.edu.au> 2023-04-10 13:16:43 +1000;
2706738b edgeR 3.41.6 - Fix doc usage lines that were too long. - Fix or update lots of URLs. by Gordon Smyth <smyth@wehi.edu.au> 2023-03-01 16:26:58 +1100;
ab0c8a0b edgeR 3.41.5 - Revise and clean-up error checking for DGEList(). by Gordon Smyth <smyth@wehi.edu.au> 2023-03-01 15:26:47 +1100;
fe774cf9 edgeR 3.41.4 - `y` is now a compulsory argument for DGEList(). Previously it defaulted to a matrix with zero rows and zero columns. by Gordon Smyth <smyth@wehi.edu.au> 2023-03-01 08:06:32 +1100;
337692d6 edgeR 3.41.3 - DGEList() is now an S3 generic function with a method for data.frames. by Gordon Smyth <smyth@wehi.edu.au> 2023-03-01 05:40:08 +1100;
ddb1cb9b (origin/RELEASE_3_16, RELEASE_3_16) Bump version to trigger rebuild and propagation of new Mac binary by J Wokaty <jwokaty@users.noreply.github.com> 2023-01-19 11:16:26 -0500;
8fd12b46 Bump version to trigger rebuild and propagation of new arm64 binary by J Wokaty <jwokaty@users.noreply.github.com> 2022-12-13 18:05:40 -0500;
7dc6dd1f edgeR 3.41.2 - Update NAMESPACE for getNormLibSizes() - Add getNormLibSizes() to calcNormFactors example. by Gordon Smyth <smyth@wehi.edu.au> 2022-12-01 22:10:20 +1100;
d7fe5d6c Rename effectiveLibSizes() to getNormLibSizes(). by Gordon Smyth <smyth@wehi.edu.au> 2022-11-07 21:16:59 +1100;
3d7dc4d0 Commit normLibSizes.R by Gordon Smyth <smyth@wehi.edu.au> 2022-11-07 21:12:09 +1100;
5b37813c New function normLibSizes() is now a synonym for calcNormFactors(). by Gordon Smyth <smyth@wehi.edu.au> 2022-11-07 21:04:02 +1100;
d87ec1f2 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 11:04:03 -0400;
0b25adcc 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 11:04:03 -0400;
8cde3aa4 Continuing edgeR 3.39.8 bug fix. by Gordon Smyth <smyth@wehi.edu.au> 2022-11-01 11:54:29 +1100;
9d4a1bb2 edgeR 3.39.8 - fix bug in plotMD() when `object` is a SummarizedExperiment. by Gordon Smyth <smyth@wehi.edu.au> 2022-11-01 09:48:38 +1100;
a6c7eefa edgeR v3.39.7 - Update NEWS.Rd - Update users' guide - Update test files by Yunshun Chen <yuchen@wehi.edu.au> 2022-10-28 16:51:53 +1100;
f5a3bb56 (origin/RELEASE_3_15, RELEASE_3_15) edgeR 3.38.4 by Gordon Smyth <smyth@wehi.edu.au> 2022-08-07 19:42:19 +1000;
5a8d1ad2 edgeR 3.39.6 by Gordon Smyth <smyth@wehi.edu.au> 2022-08-07 19:28:58 +1000;
affb2845 edgeR 3.38.3 by Gordon Smyth <smyth@wehi.edu.au> 2022-08-05 11:46:15 +1000;
867b5efa edgeR 3.39.5 by Gordon Smyth <smyth@wehi.edu.au> 2022-08-05 11:38:34 +1000;
079bfe83 edgeR 3.39.4 by Gordon Smyth <smyth@wehi.edu.au> 2022-07-31 16:16:12 +1000;
bb564574 edgeR 3.38.2 by Gordon Smyth <smyth@wehi.edu.au> 2022-07-30 11:04:48 +1000;
3cbebb35 Add note to goana.Rd about other methods. by Gordon Smyth <smyth@wehi.edu.au> 2022-07-08 11:20:46 +1000;
d2dbb91e Add Liu et al 2015 reference to voomLmFit.Rd by Gordon Smyth <smyth@wehi.edu.au> 2022-07-06 18:01:56 +1000;
b1fa8daf Edit nearestTSS.Rd by Gordon Smyth <smyth@wehi.edu.au> 2022-05-21 14:26:41 +1000;
e58bf52f edgeR 3.39.1 - Update C++ BLAS calls to account for USE_FC_LEN_T setting in R 4.3.0. by Gordon Smyth <smyth@wehi.edu.au> 2022-05-10 19:22:09 +1000;
eb5eda3f edgeR 3.39.1 - Update C++ BLAS calls to account for USE_FC_LEN_T setting in R 4.3.0. by Gordon Smyth <smyth@wehi.edu.au> 2022-05-10 18:04:20 +1000;
bff821b7 bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:01:51 +0000;
4e6141bb bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:01:51 +0000;
41497cf4 Update nearestTSS.Rd to explain resolution of multiple TSS for same gene. by Gordon Smyth <smyth@wehi.edu.au> 2022-04-23 20:28:09 +1000;
76834ca8 Update nearestTSS.Rd to specify genome version for human and mouse. by Gordon Smyth <smyth@wehi.edu.au> 2022-04-23 19:26:27 +1000;
a833e57b edgeR 3.37.4 - nearestTSS.Rd now lists explicitly all allowable values for `species`. by Gordon Smyth <smyth@wehi.edu.au> 2022-04-23 11:26:23 +1000;
313be2e6 edgeR 3.37.3 - Update NEWS.Rd. by Gordon Smyth <smyth@wehi.edu.au> 2022-04-21 22:07:18 +1000;
48bd7d3b edgeR 3.37.2 - Update NEWS.Rd - Update User's Guide - Update test files by Yunshun Chen <yuchen@wehi.edu.au> 2022-04-20 18:23:20 +1000;
be969424 If `keep.DGEList=TRUE` the `genes` data.frame is saved to the DGEList as well. by Gordon Smyth <smyth@wehi.edu.au> 2022-03-16 12:39:08 +1100;
3c92eee4 edgeR 3.37.1 - new argument `keep.DGEList` for voomLmFit(). by Gordon Smyth <smyth@wehi.edu.au> 2022-03-16 12:23:44 +1100;
8845c2f1 bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 15:52:54 +0000;
c7db03ad (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 15:52:53 +0000;
6bab9988 Bump up the version number by Yunshun Chen <yuchen@wehi.edu.au> 2021-10-21 09:57:05 +1100;
7a7dc909 Updated edgeR user's guide and the test file. by Yunshun Chen <yuchen@wehi.edu.au> 2021-10-20 11:18:38 +1100;
791233fb edgeR 3.55.2 by Gordon Smyth <smyth@wehi.edu.au> 2021-10-19 21:16:39 +1100;
28eb1e30 Complete citentry details for Chen et al (2016). by Gordon Smyth <smyth@wehi.edu.au> 2021-10-16 17:29:41 +1100;
2081679c Add Chen et al (2016) to CITATION file. by Gordon Smyth <smyth@wehi.edu.au> 2021-10-16 09:36:09 +1100;
0a0c62a7 (origin/RELEASE_3_13, RELEASE_3_13) edgeR 3.34.1 by Gordon Smyth <smyth@wehi.edu.au> 2021-09-04 10:58:09 +1000;
89deae08 Remove incorrect line from NEWS.Rd. by Gordon Smyth <smyth@wehi.edu.au> 2021-09-01 22:46:57 +1000;
51899089 Merge branch 'master' of git.bioconductor.org:packages/edgeR by Gordon Smyth <smyth@wehi.edu.au> 2021-09-01 22:34:32 +1000;
5245433a edgeR 3.35.1 by Gordon Smyth <smyth@wehi.edu.au> 2021-09-01 22:26:52 +1000;
d0d3bed2 edgeR v3.35.1 - Expand News item about plotMDS.DGEList and mention new var.explained argument. - Avoid diffSpliceDGE() return NA p-values for all zeros. by Yunshun Chen <yuchen@wehi.edu.au> 2021-09-01 22:17:48 +1000;
11c5e470 bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:41:40 +0000;
fedf54d9 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:41:40 +0000;
e92bec70 edgeR 3.33.7 by Gordon Smyth <smyth@wehi.edu.au> 2021-05-13 16:37:46 +1000;
a19c207a edgeR 3.33.6 - Restore the "bcv" method in plotMDS.DGEList(). Add an deprecation note instead. - Convert file line ends to Unix format. by Yunshun Chen <yuchen@wehi.edu.au> 2021-05-13 11:29:51 +1000;