1. RCAS
  2. Graph
Graph of RCAS
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  • 44fd977 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) 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 10:12:38 -0400;
  • 6e3cea1 (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 10:12:38 -0400;
  • 12f9502 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 10:52:30 -0400;
  • 6c7eab5 (origin/RELEASE_3_19, RELEASE_3_19) 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 10:52:30 -0400;
  • 8482e15 makeTxDbFromGRanges() has moved from GenomicFeatures to txdbmaker by Hervé Pagès <hpages.on.github@gmail.com> 2024-03-19 18:54:05 -0700;
  • 29afe07 version bump after fixing dependency issue (ggseqlogo) by borauyar <borauyar1985@gmail.com> 2024-02-04 21:30:32 +0100;
  • f3b9047 (origin/RELEASE_3_18, RELEASE_3_18) version bump by borauyar <borauyar1985@gmail.com> 2024-02-04 21:28:43 +0100;
  • ae954b5 Fix dependency issue: drop ggseqlogo; replace with seqLogo by borauyar <borauyar1985@gmail.com> 2024-02-04 21:27:45 +0100;
  • f054dd9 add import statement for seqLogo by borauyar <borauyar1985@gmail.com> 2024-02-04 21:07:02 +0100;
  • e28de05 remove import statements related to ggseqlogo by borauyar <borauyar1985@gmail.com> 2024-02-04 20:52:42 +0100;
  • 2f2eb3c update text description; motifRG no longer used by borauyar <borauyar1985@gmail.com> 2024-02-04 20:50:03 +0100;
  • d29dba4 replace ggseqlogo with seqLogo in vignettes by borauyar <borauyar1985@gmail.com> 2024-02-04 20:49:49 +0100;
  • 014fcb5 drop ggseqlogo plots, add seqLogo plots by borauyar <borauyar1985@gmail.com> 2024-02-04 20:49:20 +0100;
  • cb48471 drop ggseqlogo as dependency, add seqLogo as dependency by borauyar <borauyar1985@gmail.com> 2024-02-04 20:47:45 +0100;
  • f248f2d add new function to convert sequences to position-weight-matrices by borauyar <borauyar1985@gmail.com> 2024-02-04 20:47:13 +0100;
  • 24ef55a Merge branch 'master' into RELEASE_3_18 by borauyar <borauyar1985@gmail.com> 2023-10-30 14:00:38 +0100;
  • a1d10f3 version bump by borauyar <borauyar1985@gmail.com> 2023-10-30 13:59:20 +0100;
  • 001a791 bug fix: fixes <a href="#15">#15</a> by borauyar <borauyar1985@gmail.com> 2023-10-30 13:58:16 +0100;
  • 6b6aebe version bump after bug fix by borauyar <borauyar1985@gmail.com> 2023-10-30 12:28:09 +0100;
  • edbeab9 bug fix: add BiocManager to suggests; some methods access BiocManager functions in test/examples/vignettes by borauyar <borauyar1985@gmail.com> 2023-10-30 12:26:26 +0100;
  • f155e53 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 10:51:39 -0400;
  • 9af29aa 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 10:51:39 -0400;
  • 5304d5c 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 10:48:24 -0400;
  • 64293a9 (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 10:48:24 -0400;
  • 3ba35cb 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 11:14:07 -0400;
  • 385b33e (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 11:14:07 -0400;
  • 1eec0e3 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 15:33:58 +0000;
  • 3841e30 (origin/RELEASE_3_15, RELEASE_3_15) 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 15:33:58 +0000;
  • 8c5dd58 Pass serialized S4 instances thru updateObject() by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-21 00:45:33 -0500;
  • 34c6483 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 16:29:09 +0000;
  • 1d023c7 (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 16:29:09 +0000;
  • d6dc8f8 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 16:21:54 +0000;
  • ffebafc (origin/RELEASE_3_13, RELEASE_3_13) 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 16:21:54 +0000;
  • 3cc9d41 skip gene biotype plot in report if gene_biotype column cannot be found in GTF file by Bora Uyar <buyar@Boras-MBP.fritz.box> 2021-03-04 11:38:14 +0100;
  • 98b2d74 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 11:16:18 -0400;
  • ece9ca7 (origin/RELEASE_3_12, RELEASE_3_12) 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 11:16:18 -0400;
  • ec2d4f7 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 18:59:40 +0000;
  • 4ce5df6 (origin/RELEASE_3_11, RELEASE_3_11) 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 18:59:40 +0000;
  • 0cb2473 version bump by Bora Uyar <buyar@kempa47.mdc-berlin.net> 2020-04-22 13:51:47 +0200;
  • a5db700 reorganize the returned table from queryGff function to include more information about overlapping query regions by Bora Uyar <buyar@kempa47.mdc-berlin.net> 2020-04-22 13:51:35 +0200;
  • 01fa8b0 version bump by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-16 19:52:45 +0200;
  • 83d7290 revert back to makeCluster - forks dont work in windows by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-16 19:52:18 +0200;
  • db49674 version bump by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-12 14:19:46 +0200;
  • d237cb6 add fisher.test to import statements, update documentation by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-12 14:10:07 +0200;
  • bcc0451 print motif summary stats as a table in the report by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-12 14:01:21 +0200;
  • c4b6c0c add fisher pvalue and odds ratio for motif occurrence statistics by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-12 14:00:40 +0200;
  • 5b7a937 version bump by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-12 12:31:25 +0200;
  • 30deb42 update documentation due to roxygen update in formatting by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-12 12:31:04 +0200;
  • 930d362 use makeForkCluster instead of makeCluster by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-04-12 12:30:13 +0200;
  • 84c93c7 update version + date by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-03-15 21:15:38 +0100;
  • 8a02a09 simplify motif plotting code by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-03-15 20:57:52 +0100;
  • 47f7c7b use factors for dependent variable by Bora Uyar <buyar@Boras-MBP.fritz.box> 2020-03-15 20:57:30 +0100;
  • 2809ae3 version bump by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-09 15:01:16 +0100;
  • ac2772f turn on vignette evaluation by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-09 15:00:31 +0100;
  • 59d03b3 improve doc by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-09 14:59:48 +0100;
  • 6f1267e improve doc by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-09 14:59:31 +0100;
  • 0e8fc28 Undeprecate by lshep <lori.shepherd@roswellpark.org> 2020-03-05 15:32:41 -0500;
  • 5068eec version bump by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 19:20:28 +0100;
  • 70ff185 update NEWS by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 18:40:43 +0100;
  • b3e1e9d version bump by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 18:33:18 +0100;
  • a8761d6 fix warnings/errors about namespaces by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 18:28:34 +0100;
  • 8aeead6 remove built-in genesets object by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 17:10:17 +0100;
  • 1efe5c6 update tests by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 17:07:57 +0100;
  • 027346d update abstract and dependencies by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 17:07:31 +0100;
  • c06cdbd update README and single-sample analysis vignette by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 16:52:03 +0100;
  • fbed287 update motif functions - add checks for null results. update docs by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 16:32:13 +0100;
  • 96974d3 adapt meta-analysis functions and scripts to updated motif functions by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-04 16:31:34 +0100;
  • 13206d7 Parameterize BSgenome imports - now all BSgenome versions are supported by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 23:29:30 +0100;
  • 170b455 update tests for motif discovery by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 22:15:07 +0100;
  • 71e27c5 remove tests for topGO and msigdb by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 22:11:59 +0100;
  • 09a49f8 updated docs by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 22:09:25 +0100;
  • 03a18f1 update runReport function to replace deprecated enrichment functions by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 22:09:08 +0100;
  • c6ee0f1 remove unnecessary imports/suggests by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 22:08:23 +0100;
  • 026a99d export findEnrichedFunctions by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 22:07:09 +0100;
  • 0be2c07 deprecate topGO and msigdb enrichment functions and replace with gprofiler2::gost by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 21:16:48 +0100;
  • c2ebed1 remove private unused function by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 21:00:11 +0100;
  • 183ddf1 deprecate function: calculateCoverageProfileFromTxdb by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 20:59:45 +0100;
  • 02c2c26 deprecated function: calculateCoverageProfileListFromTxdb by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 20:57:22 +0100;
  • aa31100 deprecate getTxdbFeatures function by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 20:54:50 +0100;
  • 85fe604 update report script to accommodate changes in motif discovery functions by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 19:57:26 +0100;
  • 637a043 simplify discoverFeatureSpecificMotifs function by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 19:56:58 +0100;
  • 7550328 adapt motif related functions to remove motifRG dependency by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-03 17:53:54 +0100;
  • 09ec621 update imported dependencies by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-02 17:19:35 +0100;
  • 8645e48 update docs for deprecated function by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-02 17:19:08 +0100;
  • d51988d remove docs for runMotifRG by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-02 17:08:05 +0100;
  • b1ac700 update documentation by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-02 17:07:26 +0100;
  • 386ebc4 update roxygen version by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-02 17:07:04 +0100;
  • 87fc6e8 Deprecate function runMotifRG - add new functions to 1. generate kmers 2. build a classifier to find important k-mers with mismatches 3. extract matching sequences for top motifs by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-02 15:34:05 +0100;
  • 4adf41e remove motifRG from dependencies by Bora Uyar <buyar@Boras-MBP.mdc-berlin.net> 2020-03-02 15:33:36 +0100;
  • 6d87238 Deprecate Package by lshep <lori.shepherd@roswellpark.org> 2020-01-06 12:20:09 -0500;
  • 7ffde2d 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 13:41:55 -0400;
  • 8b40ab4 (origin/RELEASE_3_10, RELEASE_3_10) 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 13:09:55 -0400;
  • 909750b (origin/RELEASE_3_9, RELEASE_3_9) version bump by borauyar <bora.uyar@mdc-berlin.de> 2019-07-10 16:22:11 +0200;
  • 1ef2f79 Bugfix: fix bug due to changes in biomaRt::getLDS arguments by borauyar <bora.uyar@mdc-berlin.de> 2019-07-10 16:21:36 +0200;
  • 6e1c0e1 version bump by borauyar <bora.uyar@mdc-berlin.de> 2019-07-10 16:22:11 +0200;
  • 22ba607 Bugfix: fix bug due to changes in biomaRt::getLDS arguments by borauyar <bora.uyar@mdc-berlin.de> 2019-07-10 16:21:36 +0200;
  • e20482f bump x.y.z versions to odd y after creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 12:13:46 -0400;
  • 258873f bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 11:54:03 -0400;
  • e1edab9 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:36 -0400;
  • a2f099e (origin/RELEASE_3_8, RELEASE_3_8) bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:42:02 -0400;