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Graph ofedgeR

ddb1cb9b2 (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;
8fd12b464 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;
7dc6dd1fc (HEAD -> master, origin/master, origin/HEAD) 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;
d7fe5d6c8 Rename effectiveLibSizes() to getNormLibSizes(). by Gordon Smyth <smyth@wehi.edu.au> 2022-11-07 21:16:59 +1100;
3d7dc4d0f Commit normLibSizes.R by Gordon Smyth <smyth@wehi.edu.au> 2022-11-07 21:12:09 +1100;
5b37813c0 New function normLibSizes() is now a synonym for calcNormFactors(). by Gordon Smyth <smyth@wehi.edu.au> 2022-11-07 21:04:02 +1100;
d87ec1f2f 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;
0b25adcc6 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;
8cde3aa4b Continuing edgeR 3.39.8 bug fix. by Gordon Smyth <smyth@wehi.edu.au> 2022-11-01 11:54:29 +1100;
9d4a1bb21 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;
a6c7eefa0 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;
f5a3bb568 (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;
5a8d1ad2e edgeR 3.39.6 by Gordon Smyth <smyth@wehi.edu.au> 2022-08-07 19:28:58 +1000;
affb28452 edgeR 3.38.3 by Gordon Smyth <smyth@wehi.edu.au> 2022-08-05 11:46:15 +1000;
867b5efa1 edgeR 3.39.5 by Gordon Smyth <smyth@wehi.edu.au> 2022-08-05 11:38:34 +1000;
079bfe839 edgeR 3.39.4 by Gordon Smyth <smyth@wehi.edu.au> 2022-07-31 16:16:12 +1000;
bb564574f edgeR 3.38.2 by Gordon Smyth <smyth@wehi.edu.au> 2022-07-30 11:04:48 +1000;
3cbebb35a Add note to goana.Rd about other methods. by Gordon Smyth <smyth@wehi.edu.au> 2022-07-08 11:20:46 +1000;
d2dbb91e5 Add Liu et al 2015 reference to voomLmFit.Rd by Gordon Smyth <smyth@wehi.edu.au> 2022-07-06 18:01:56 +1000;
b1fa8daf9 Edit nearestTSS.Rd by Gordon Smyth <smyth@wehi.edu.au> 2022-05-21 14:26:41 +1000;
e58bf52f3 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;
eb5eda3fa 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;
bff821b71 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;
4e6141bb5 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;
41497cf4c 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;
76834ca89 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;
a833e57b4 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;
313be2e6a edgeR 3.37.3 - Update NEWS.Rd. by Gordon Smyth <smyth@wehi.edu.au> 2022-04-21 22:07:18 +1000;
48bd7d3ba 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;
be9694248 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;
3c92eee4e edgeR 3.37.1 - new argument `keep.DGEList` for voomLmFit(). by Gordon Smyth <smyth@wehi.edu.au> 2022-03-16 12:23:44 +1100;
8845c2f12 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;
c7db03add (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;
6bab99880 Bump up the version number by Yunshun Chen <yuchen@wehi.edu.au> 2021-10-21 09:57:05 +1100;
7a7dc9093 Updated edgeR user's guide and the test file. by Yunshun Chen <yuchen@wehi.edu.au> 2021-10-20 11:18:38 +1100;
791233fbe edgeR 3.55.2 by Gordon Smyth <smyth@wehi.edu.au> 2021-10-19 21:16:39 +1100;
28eb1e30c Complete citentry details for Chen et al (2016). by Gordon Smyth <smyth@wehi.edu.au> 2021-10-16 17:29:41 +1100;
2081679c2 Add Chen et al (2016) to CITATION file. by Gordon Smyth <smyth@wehi.edu.au> 2021-10-16 09:36:09 +1100;
0a0c62a7f (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;
89deae081 Remove incorrect line from NEWS.Rd. by Gordon Smyth <smyth@wehi.edu.au> 2021-09-01 22:46:57 +1000;
518990896 Merge branch 'master' of git.bioconductor.org:packages/edgeR by Gordon Smyth <smyth@wehi.edu.au> 2021-09-01 22:34:32 +1000;
5245433a9 edgeR 3.35.1 by Gordon Smyth <smyth@wehi.edu.au> 2021-09-01 22:26:52 +1000;
d0d3bed2c 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;
11c5e4705 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;
fedf54d9a 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;
e92bec70d edgeR 3.33.7 by Gordon Smyth <smyth@wehi.edu.au> 2021-05-13 16:37:46 +1000;
a19c207a1 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;
43d8f8175 edgeR 3.33.5 - Remove the "BCV" method in plotMDS.DGEList(); - Update the edgeR User's Guide; - Update NEWS.Rd; - Update test files. by Yunshun Chen <yuchen@wehi.edu.au> 2021-05-12 10:31:55 +1000;
779cf9946 edgeR 3.33.4 by Gordon Smyth <smyth@wehi.edu.au> 2021-05-10 21:36:45 +1000;
0cb43c1a4 edgeR 3.33.3 by Gordon Smyth <smyth@wehi.edu.au> 2021-03-03 16:15:59 +1100;
2eb3f8e79 Convert file line ends to Unix format (no change to code). by Gordon Smyth <smyth@wehi.edu.au> 2021-02-16 16:03:20 +1100;
b591c2d2c edgeR 3.33.2 by Gordon Smyth <smyth@wehi.edu.au> 2021-02-16 15:55:07 +1100;
b881d801d (origin/RELEASE_3_12, RELEASE_3_12) edgeR 3.32.1 - Fix bug in voomLmFit() whereby zeros were sometimes incorrectly identified due to floating point errors. - Check for duplicated names before setting row.names(genes) equal to row.names(counts) in DGEList(). - Use message() instead of cat() in estimateDisp(). - Revise calcNormFactors.Rd including change of title. by Gordon Smyth <smyth@wehi.edu.au> 2021-01-14 16:54:32 +1100;
db2e781ef Fix typo. No change to functionality. by Gordon Smyth <smyth@wehi.edu.au> 2021-01-14 16:49:51 +1100;
a966bd831 edgeR 3.33.1 - Fix bug in voomLmFit() whereby zeros were sometimes incorrectly identified due to floating point errors. - Check for duplicated names before setting row.names(genes) equal to row.names(counts) in DGEList(). - Use message() instead of cat() in estimateDisp(). - Revise calcNormFactors.Rd including change of title. by Gordon Smyth <smyth@wehi.edu.au> 2021-01-11 21:17:30 +1100;
03ec04997 bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:34:20 -0400;
3695f2374 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:34:19 -0400;
bd7882613 edgeR v3.31.7 - Fixed a bug in cpm.DGEList() and rpkm.DGEList(). by Yunshun Chen <yuchen@wehi.edu.au> 2020-10-22 19:36:47 +1100;
0b0ad1209 edgeR 3.31.6 by Gordon Smyth <smyth@wehi.edu.au> 2020-10-20 21:59:39 +1100;
7c97a72ff Updated edgeR user's guide. Updated edgeR test file outputs. by Yunshun Chen <yuchen@wehi.edu.au> 2020-10-20 16:40:48 +1100;
99df7996e Fixed a typo in edgeR user's guide. by Yunshun Chen <yuchen@wehi.edu.au> 2020-10-16 15:56:37 +1100;
d9f4ce438 edgeR v3.31.5 - cpm.default() and rpkm.default() now accept offset. - scaleOffset() now accepts CompressedMatrix offset and accounts for norm.factors. - Change default choice for refColumn in calcNormFactors() with method="TMMwsp". The new method chooses the column with the largest sum of sqrt-counts. - processAmplicons() can now accommodate data from newer screens that use a staggered primer design. - Fixed a bug that diffSpliceDGE() accept more than one coef. It now gives a warning if more than one coef or contrast is supplied. It only uses the first. - Updated edgeR user's guide and NEWS.Rd. by Yunshun Chen <yuchen@wehi.edu.au> 2020-10-15 10:24:25 +1100;
2ffbe332f edgeR 3.31.4 by Gordon Smyth <smyth@wehi.edu.au> 2020-06-10 19:22:02 +1000;
4f3fd493a edgeR 3.31.3 by Gordon Smyth <smyth@wehi.edu.au> 2020-06-02 19:19:08 +1000;
7a3a272f8 (origin/RELEASE_3_11, RELEASE_3_11) edgeR 3.30.3 by Gordon Smyth <smyth@wehi.edu.au> 2020-06-02 19:01:09 +1000;
f5d110d2c Rerun all User's Guide case studies. by Gordon Smyth <smyth@wehi.edu.au> 2020-06-02 13:04:32 +1000;
aeffee8c2 Rerun all User's Guide case studies. by Gordon Smyth <smyth@wehi.edu.au> 2020-06-02 13:03:28 +1000;
a84681ded edgeR 3.31.2 by Gordon Smyth <smyth@wehi.edu.au> 2020-06-02 12:25:23 +1000;
d0f4efdde edgeR 3.30.2 by Gordon Smyth <smyth@wehi.edu.au> 2020-06-02 12:13:36 +1000;
594a34851 edgeR 3.31.1 by Gordon Smyth <smyth@wehi.edu.au> 2020-05-31 12:00:44 +1000;
09e7bb4e6 edgeR 3.30.1 by Gordon Smyth <smyth@wehi.edu.au> 2020-05-31 11:59:32 +1000;
7fd097f1a bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:17:56 +0000;
8f037f40f bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:17:56 +0000;
25a069c77 edgeR 3.29.2 - New function voomLmFit() that combines the limma voom-lmFit pipeline with loss of residual df due to zero counts as for glmQLFit(); - New function SE2DGEList() to convert a SummarizedExperiment object into a DGEList object; - S3 methods for SummarizedExperiment objects are added to the following functions: aveLogCPM(), calcNormFactors(), cpm(), cpmByGroup(), estimateDisp(), filterByExpr(), glmFit(), glmQLFit(), plotMD(), plotMDS(), predFC(), rowsum(), rpkm(), rpkmByGroup() and sumTechReps(); - New cpm() and rpkm() methods for DGEGLM and DGELRT objects; - New function effectiveLibSizes() to extract normalized library sizes from an edgeR data object or fitted model object; - Added a time course case study in user's guide. by Yunshun Chen <yuchen@wehi.edu.au> 2020-04-25 19:33:04 +1000;
b9862ccbf Fix date entry (should be 2020 instead of 2019). by Gordon Smyth <smyth@wehi.edu.au> 2020-03-22 11:53:05 +1100;
3e0d7a78e (origin/RELEASE_3_10) edgeR 3.28.1 by Gordon Smyth <smyth@wehi.edu.au> 2020-02-26 19:21:46 +1100;
3ac81ee04 Ran qpdf on edgeRUsersGuide.pdf by Gordon Smyth <smyth@wehi.edu.au> 2020-02-26 18:36:42 +1100;
fc6e1a185 edgeR 3.29.1 by Gordon Smyth <smyth@wehi.edu.au> 2020-02-26 18:34:48 +1100;
fa1e83d38 bump x.y.z version to odd y after creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:34:51 -0400;
e4a61e04d bump x.y.z version to even y prior to creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:07:57 -0400;
f985083a6 edgeR 3.27.14 - Removed the "mixed.df" argument and added the "locfit.mixed" option to "trend.method" in estimateDisp() and WLEB(). - Update NEWS.Rd, test files and edgeR user's guide. by Yunshun Chen <yuchen@wehi.edu.au> 2019-10-21 14:06:52 +1100;
836809e04 (origin/RELEASE_3_9, RELEASE_3_9) * edgeR 3.26.8 - In catchSalmon(), use num_valid_targets if num_targets not found in Salmon output. - Remove calcNormFactors.Rd Note about changing default method. by Gordon Smyth <smyth@wehi.edu.au> 2019-09-01 10:40:08 +1000;
8b11065d4 Edit to users guide. - Correct date on users guide title page. by Gordon Smyth <smyth@wehi.edu.au> 2019-09-01 10:36:15 +1000;
e91309ea6 edgeR 3.27.13 - In catchSalmon(), use num_valid_targets if num_targets not found in Salmon output. - Remove calcNormFactors.Rd Note about changing default method. by Gordon Smyth <smyth@wehi.edu.au> 2019-09-01 10:18:18 +1000;
9a659689e edgeR 3.26.7 by Gordon Smyth <smyth@wehi.edu.au> 2019-08-13 20:45:54 +1000;
98d10bf23 edgeR 3.27.12 - User's Guide: fix design matrix on page 34. - Add head() and tail() methods for edgeR classes. - Remove Davis from maintainer list. - Add see-also reference for plotMeanVar2() from plotMeanVar(). - Rewrite dglmStdResid() and rename to plotMeanVar2(). New version is shorter and faster, easier to understand and handles leverages more accurately. - getDispersions() is no longer exported because its output is already contained in output from dglmStdResid(). - Ensure that NAs are of the appropriate class. - rep_len(x,l) instead of rep(x,length=l). - In glmFit check for NA dispersion values, as might be returned by estimateDisp() when there are no residual df. by Gordon Smyth <smyth@wehi.edu.au> 2019-08-13 20:39:44 +1000;
866633a9a edgeR 3.27.11 - Add two new arguments to filterByExpr() to allow users to change parameters previously hard-wired. by Gordon Smyth <smyth@wehi.edu.au> 2019-08-04 17:27:45 +1000;
b26e98ada * edgeR 3.26.6 by Gordon Smyth <smyth@wehi.edu.au> 2019-07-28 19:06:50 +1000;
61af6ad04 edgeR 3.27.10 by Gordon Smyth <smyth@wehi.edu.au> 2019-07-28 18:43:35 +1000;
8b145abfe edgeR 3.27.9 - Lengthen author list in DESCRIPTION file to include people who contributed particular functions. - Update Davis McCarthy's email address in maintainer list. by Gordon Smyth <smyth@wehi.edu.au> 2019-07-19 15:06:20 +1000;
aa56bc013 Dependency updates - edgeR depends on limma 3.41.5 so that plotMD.DGELRT and plotMD.ExactText will work as intended on TestResults objects. - edgeR depends on R 3.6.0 because of changes to `ties` argument of approx() in limma 3.39.16 and edgeR 3.27.2. by Gordon Smyth <smyth@wehi.edu.au> 2019-07-18 17:21:27 +1000;
251d54ca8 Update Aaron's email address. Remove emails for authors. by Gordon Smyth <smyth@wehi.edu.au> 2019-07-18 16:59:40 +1000;
4cc6babd8 edgeR 3.27.8 - Update romer.DGEList.Rd reference with final publication details. - Change nrot default in roast and mroast to 9999 instead of 1e4 to that two-sided p-value is nicer. by Gordon Smyth <smyth@wehi.edu.au> 2019-07-18 13:06:56 +1000;
88279e4f2 Merge branch 'master' of git.bioconductor.org:packages/edgeR by Gordon Smyth <smyth@wehi.edu.au> 2019-07-18 13:03:29 +1000;
b372adc23 roast.DGEList() and mroast.DGEList() now have an nrot argument which is passed roast.default or mroast.default. Previously the number of rotations could not be set. by Gordon Smyth <smyth@wehi.edu.au> 2019-07-16 20:15:23 +1000;
fb3f8a227 roast.DGEList() and mroast.DGEList() now pass the nrot argument to roast.default. Previously the nrot argument was ignored. by Gordon Smyth <smyth@wehi.edu.au> 2019-07-16 20:15:23 +1000;
a0f6dba83 edgeR 3.26.5 - Bug fix to rpkmByGroup by Gordon Smyth <smyth@wehi.edu.au> 2019-06-21 14:14:56 +1000;
8b7423ce2 edgeR 3.37.6 - Bug fix to rpkmByGroup by Gordon Smyth <smyth@wehi.edu.au> 2019-06-21 13:16:04 +1000;
0b2d8840c Arguments 'values' and 'col' are no longer needed for plotMD.DGELRT and plotMD.ExactTest because of changes to plotWithHighlights() to handle TestResults objects. by Gordon Smyth <smyth@wehi.edu.au> 2019-06-17 18:17:29 +1000;
430c45336 edgeR 3.27.4 - Fix the recent revision to goana.DGELRT and kegga.DGELRT to not assume a test.df component in the DGELRT object. by Gordon Smyth <smyth@wehi.edu.au> 2019-05-27 19:26:36 +1000;