Bioconductor Code: ChIPpeakAnno

Graph of ChIPpeakAnno

cfbf3356 (HEAD -> devel, origin/devel, origin/HEAD) Update Jianhong's email address by JIANHONG OU <jianhong@users.noreply.github.com> 2025-01-03 09:42:19 -0500;
0f4b7da8 (origin/master) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2024-10-29 09:32:01 -0400;
faf2e4fb (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2024-10-29 09:32:01 -0400;
c8e72cd3 Fix the documentation for Vennerable by JIANHONG OU <jianhong@users.noreply.github.com> 2024-08-15 08:19:40 -0400;
e2533c70 Fix the documentation for summarizePatterInPeaks by JIANHONG OU <jianhong@users.noreply.github.com> 2024-07-05 11:36:54 -0400;
6b073766 (origin/RELEASE_3_19, RELEASE_3_19) fix a bug that FUN parameter is not passed to the function of addMetadata. by JIANHONG OU <jianhong@users.noreply.github.com> 2024-07-03 13:41:54 -0400;
b0405a13 fix the document. by JIANHONG OU <jianhong@users.noreply.github.com> 2024-07-03 13:38:14 -0400;
0eea3734 bump the version. by JIANHONG OU <jianhong@users.noreply.github.com> 2024-07-03 11:29:42 -0400;
991067b4 fix the bug in addMetadata. by JIANHONG OU <jianhong@users.noreply.github.com> 2024-07-03 11:23:47 -0400;
1ad9ed54 Merge pull request <a href="#42">#42</a> from hukai916/devel by JIANHONG OU <jianhong@users.noreply.github.com> 2024-07-03 11:17:49 -0400;
79c3a83e Update R/assignChromosomeRegion.R by JIANHONG OU <jianhong@users.noreply.github.com> 2024-07-03 11:17:33 -0400;
e2cd915d add unique(promoter()) in genomicElementDistribution() to match that in assignChromosomeRegion.R by Kai Hu <hukai916@gmail.com> 2024-06-07 18:31:26 -0400;
8fc6473b Merge remote-tracking branch 'upstream/devel' into devel by JIANHONG OU <jianhong@users.noreply.github.com> 2024-05-06 08:28:09 -0400;
d19cc742 bump x.y.z version to odd y following creation of RELEASE_3_19 branch by J Wokaty <jwokaty@users.noreply.github.com> 2024-04-30 10:20:21 -0400;
26e03e37 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by J Wokaty <jwokaty@users.noreply.github.com> 2024-04-30 10:20:21 -0400;
65471718 Merge remote-tracking branch 'upstream/devel' into devel by JIANHONG OU <jianhong@users.noreply.github.com> 2024-04-26 14:19:33 -0400;
118d25ab Update by importing pwalign by JIANHONG OU <jianhong@users.noreply.github.com> 2024-04-26 14:18:22 -0400;
9e0412d3 pairwiseAlignment() has moved from Biostrings to pwalign by Hervé Pagès <hpages.on.github@gmail.com> 2024-04-23 11:14:00 -0700;
105ec602 (origin/RELEASE_3_18, RELEASE_3_18) Merge pull request <a href="#40">#40</a> from hukai916/RELEASE_3_18 by JIANHONG OU <jianhong@users.noreply.github.com> 2024-02-15 15:06:09 -0500;
5343f7b3 minor fix to resolve the seqlevelsStyle() issue by Kai Hu <hukai916@gmail.com> 2024-02-12 22:18:20 -0500;
8603e305 Merge pull request <a href="#39">#39</a> from hukai916/RELEASE_3_18 by JIANHONG OU <jianhong@users.noreply.github.com> 2024-02-12 16:21:53 -0500;
3bbe6598 minor fixes for 3.36.0 by Kai Hu <hukai916@gmail.com> 2024-02-08 15:29:13 -0500;
58a122cb update news and bump up the version. by JIANHONG OU <jianhong@users.noreply.github.com> 2024-01-29 08:57:31 -0500;
48cc65cb Merge pull request <a href="#38">#38</a> from hukai916/devel by JIANHONG OU <jianhong@users.noreply.github.com> 2024-01-24 13:05:13 -0500;
d3f84159 handle the biofilecache error by Kai Hu <hukai916@gmail.com> 2024-01-22 12:37:20 -0500;
e9d4a71d fix the import package issues. by JIANHONG OU <jianhong@users.noreply.github.com> 2024-01-10 17:31:30 -0500;
330d612b Merge pull request <a href="#37">#37</a> from hukai916/devel by JIANHONG OU <jianhong@users.noreply.github.com> 2024-01-10 14:19:09 -0500;
b3000bc5 address Jianhong review comments by Kai Hu <hukai916@gmail.com> 2024-01-09 20:52:33 -0500;
6481e030 update vignettes, summarizePatternInPeaks, bump to 3.38.1, etc. by Kai Hu <hukai916@gmail.com> 2024-01-05 09:05:25 -0500;
df99dece update the version number. by JIANHONG OU <jianhong@users.noreply.github.com> 2023-11-20 12:21:30 -0500;
8c437d40 Merge pull request <a href="#33">#33</a> from JunhuiLi1017/devel by JIANHONG OU <jianhong@users.noreply.github.com> 2023-11-20 12:06:27 -0500;
c180b18d fix textthat by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-11-16 10:28:37 -0500;
d87a36d1 fix document in oligoNucleotideEnrichment.R by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-11-14 15:25:44 -0500;
ae30a71f removed LICENSE by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-11-14 15:14:11 -0500;
d14a3739 Merge branch 'jianhong:devel' into devel by JunhuiLi <31299960+JunhuiLi1017@users.noreply.github.com> 2023-11-14 14:52:45 -0500;
7cf869b2 updated code of function oligoNucleotideEnrichment and added unit test by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-11-14 14:51:21 -0500;
f8523e75 updated code of function oligoNucleotideEnrichment and added unit test by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-11-14 14:50:30 -0500;
c1e6ecc7 export disable.logging parameter for venn.diagram called by makeVennDiagram. by JIANHONG OU <jianhong@users.noreply.github.com> 2023-11-07 09:48:01 -0500;
81d40a42 Merge branch 'devel' of github.com:JunhuiLi1017/ChIPpeakAnno into devel update in oligoNucleotideEnrichment.R by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-11-06 14:08:10 -0500;
1d99e326 update code in oligoNucleotideEnrichment.R; Namespace; Description by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-11-06 14:06:38 -0500;
ab5e85c6 fix oligoNucleotideEnrichment.R by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-11-06 14:00:20 -0500;
92deb7aa Merge branch 'jianhong:devel' into devel by JunhuiLi <31299960+JunhuiLi1017@users.noreply.github.com> 2023-11-03 14:47:18 -0400;
5c947077 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 09:42:19 -0400;
bf45c7be 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 09:42:19 -0400;
85eb8776 add oligoNucleotideEnrichment;edit NAMESPACE by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-09-01 16:44:25 -0400;
3297e878 add oligoNucleotideEnrichment by JunhuiLi1017 <junhuili@cau.edu.cn> 2023-09-01 16:41:40 -0400;
d2136538 merge updates from Kai. by JIANHONG OU <jianhong@users.noreply.github.com> 2023-07-25 10:57:28 -0400;
3127155d Merge pull request <a href="#32">#32</a> from hukai916/master by JIANHONG OU <jianhong@users.noreply.github.com> 2023-07-25 10:55:10 -0400;
dc083df3 update documenation and .Rd; move NEWS to top-level by hukai916 <31452631+hukai916@users.noreply.github.com> 2023-07-24 17:19:18 -0400;
8af6a7d9 update doc by hukai916 <31452631+hukai916@users.noreply.github.com> 2023-07-21 17:21:17 -0400;
a0438737 revert it back. by JIANHONG OU <jianhong@users.noreply.github.com> 2023-07-20 16:50:59 -0400;
84d3d38a fix the order issue when "both" method is used for annotatePeakInBatch. by JIANHONG OU <jianhong@users.noreply.github.com> 2023-07-20 11:43:10 -0400;
1a47186c (origin/RELEASE_3_17, RELEASE_3_17) fix the version number. by JIANHONG OU <jianhong@users.noreply.github.com> 2023-04-26 18:52:20 -0400;
71289ee8 ignore logging for venn.diagram. by JIANHONG OU <jianhong@users.noreply.github.com> 2023-04-26 18:35:48 -0400;
46bdcd80 import oligonucleotideFrequency from Biostrings by JIANHONG OU <jianhong@users.noreply.github.com> 2023-04-26 18:26:47 -0400;
ee9d472c fix the seqlevelsStyle check for custom genome. by JIANHONG OU <jianhong@users.noreply.github.com> 2023-04-26 18:19:23 -0400;
6809c61f Merge pull request <a href="#31">#31</a> from hukai916/master by JIANHONG OU <jianhong@users.noreply.github.com> 2023-04-26 11:05:24 -0400;
9865ee42 add seqlevelsStyle check for custom species by hukai916 <31452631+hukai916@users.noreply.github.com> 2023-04-26 10:28:17 -0400;
6f670e80 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 09:49:12 -0400;
e82d135d 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 09:49:12 -0400;
d4d3dfbe Merge branch 'jianhong:devel' into master by hukai916 <31452631+hukai916@users.noreply.github.com> 2023-03-15 12:01:16 -0400;
5c22076f minor by hukai916 <31452631+hukai916@users.noreply.github.com> 2023-03-15 11:55:47 -0400;
62b034d2 handle edge cases by hukai916 <31452631+hukai916@users.noreply.github.com> 2023-03-15 11:38:36 -0400;
88d5adae update the documentation for enrichment analysis by JIANHONG OU <jianhong@users.noreply.github.com> 2023-03-14 15:02:32 -0400;
8e9b7b90 Merge pull request <a href="#29">#29</a> from hukai916/master by JIANHONG OU <jianhong@users.noreply.github.com> 2023-03-14 14:47:20 -0400;
66d0b444 Merge remote-tracking branch 'upstream/master' by hukai916 <31452631+hukai916@users.noreply.github.com> 2023-03-14 12:00:53 -0400;
a26b66fa update feature_id_type error prompt to be more informative; deprecate KEGG.db by hukai916 <31452631+hukai916@users.noreply.github.com> 2023-03-14 11:52:51 -0400;
47b6a15c Merge pull request <a href="#24">#24</a> from jianhong/revert-23-master by JIANHONG OU <jianhong@users.noreply.github.com> 2022-12-21 16:06:07 -0500;
90845ec6 Revert "oligoNucleotideEnrichment function is added for oligoNucleotide enric…" by JIANHONG OU <jianhong@users.noreply.github.com> 2022-12-21 16:05:53 -0500;
32341983 Merge pull request <a href="#23">#23</a> from JunhuiLi1017/master by JIANHONG OU <jianhong@users.noreply.github.com> 2022-12-21 15:00:26 -0500;
c6d0d457 oligoNucleotideEnrichment function is added for oligoNucleotide enrichment analysis by JunhuiLi1017 <junhuili@cau.edu.cn> 2022-12-09 20:17:27 -0500;
2c08eb8e update the disjointExons to exonicParts for ensembldb. by JIANHONG OU <jianhong@users.noreply.github.com> 2022-11-12 17:40:09 -0500;
2248ee8e 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 11:04:34 -0400;
016661fc (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 11:04:34 -0400;
12513f12 remove the limitation of sequence length for oligoFrequency function. by JIANHONG OU <jianhong@users.noreply.github.com> 2022-10-24 13:45:37 -0400;
465375d0 support 'csv' format for 'toGRanges' by JIANHONG OU <jianhong@users.noreply.github.com> 2022-08-17 10:53:56 -0400;
f46886fc Merge pull request <a href="#20">#20</a> from hukai916/master by JIANHONG OU <jianhong@users.noreply.github.com> 2022-08-17 09:44:41 -0400;
75bb5e20 use 'entrez_id' instead of 'EntrezID' for getEnrichedPATH() output by JIANHONG OU <jianhong@users.noreply.github.com> 2022-08-10 09:11:21 -0400;
af603222 Merge pull request <a href="#19">#19</a> from hukai916/master by JIANHONG OU <jianhong@users.noreply.github.com> 2022-08-08 17:40:57 -0400;
f358fc5e (origin/RELEASE_3_15, RELEASE_3_15) add parameter check of proximal.promoter.cutoff and immediate.downstream.cutoff for assignChromosomeRegion by JIANHONG OU <jianhong@users.noreply.github.com> 2022-06-06 14:12:10 -0400;
841797aa add parameter check of proximal.promoter.cutoff and immediate.downstream.cutoff for assignChromosomeRegion by JIANHONG OU <jianhong@users.noreply.github.com> 2022-06-06 13:05:24 -0400;
704a4740 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 15:03:21 +0000;
f5b7c4e4 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 15:03:21 +0000;
940222cc update jianhong's email. by JIANHONG OU <jianhong@users.noreply.github.com> 2022-04-15 06:35:09 -0400;
5d4f368c update the pipeline documentation to avoid the error when converting the GRanges object to data.frame. by JIANHONG OU <jianhong@users.noreply.github.com> 2022-03-17 14:15:04 -0400;
b25b79ce (origin/RELEASE_3_14, RELEASE_3_14) handle the error of "non-standard bed file" by JIANHONG OU <jianhong@users.noreply.github.com> 2022-02-04 15:06:47 -0500;
84091f2e handle the error "non standard bed file." by JIANHONG OU <jianhong@users.noreply.github.com> 2022-02-04 15:03:54 -0500;
a4147094 bump up version number. by JIANHONG OU <jianhong@users.noreply.github.com> 2022-01-06 13:23:08 -0500;
c55caef6 Merge branch 'master' of git.bioconductor.org:packages/ChIPpeakAnno by JIANHONG OU <jianhong@users.noreply.github.com> 2022-01-05 17:06:57 -0500;
9d488478 fix the error: trying to generate an object from a virtual class "DataFrame". by JIANHONG OU <jianhong@users.noreply.github.com> 2022-01-05 17:05:45 -0500;
75622aee Pass serialized S4 instances thru updateObject() by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-17 12:32:25 -0800;
e4372a63 fix the NA values in background group of enriched function. by JIANHONG OU <jianhong@users.noreply.github.com> 2021-11-10 10:37:54 -0500;
7223b567 add subGroupComparison parameter to get EnrichedGO and getEnrichedPATH. by JIANHONG OU <jianhong@users.noreply.github.com> 2021-11-10 10:13:07 -0500;
118e37c1 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 15:54:17 +0000;
da1bfa15 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 15:54:17 +0000;
3c2c9fb8 Fix the erro "!anyNA(m32) is not TRUE" in seqlevelsStyle is not handled. by JIANHONG OU <jianhong@users.noreply.github.com> 2021-10-19 09:12:15 -0400;
5104b7df (origin/RELEASE_3_13, RELEASE_3_13) Fix the error undefined columns selected in enrichment Plot by JIANHONG OU <jianhong@users.noreply.github.com> 2021-09-09 15:41:30 -0400;