1. regutools
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Graph of regutools
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  • 852059b (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 11:22:02 -0400;
  • 5db6548 (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 11:22:02 -0400;
  • c561af8 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 11:17:58 -0400;
  • a823588 (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 11:17:58 -0400;
  • cdbd584 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 11:22:01 -0400;
  • 329ca37 (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 11:22:01 -0400;
  • 01322b5 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 16:05:06 +0000;
  • 65b3988 (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 16:05:06 +0000;
  • c4d9394 Used biocthis::use_bioc_github_action("RELEASE_3_14") by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-11-22 22:51:31 -0500;
  • c08567c Get regutools ready for the switch to virtual DataFrame (in S4Vectors package) by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-15 20:47:11 -0800;
  • ebe082b 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 16:59:29 +0000;
  • 3795415 (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 16:59:29 +0000;
  • 11e37e9 match biocthis 1.3.7 after noticing https://github.com/ComunidadBioInfo/cdsb2021_scRNAseq/commit/7447618a7731d9ba13f358aceda926b195706c20 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-08-09 20:14:56 -0400;
  • 55dbae2 Ignore for now on BiocCheck by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-08-05 14:21:40 -0400;
  • 10d4820 v1.5.1 -- match bioc 1.3.6 and fix https://github.com/lcolladotor/derfinder/pull/42 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-08-05 13:29:07 -0400;
  • 6a72907 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 16:52:12 +0000;
  • fe87b86 (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 16:52:12 +0000;
  • 4c29caf (origin/RELEASE_3_12, RELEASE_3_12) Fix BiocCheck issue on linux by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-18 19:17:39 -0500;
  • 7a252b0 Fix BiocCheck issue on linux by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-18 19:17:39 -0500;
  • de4a10a Drop knitcitations from bib by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-18 14:23:30 -0500;
  • 37137a7 Drop knitcitations from bib by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-18 14:23:30 -0500;
  • 4848c99 merge with 10.8 db change by Joselyn Chavez <joselynchavezf@gmail.com> 2020-12-07 02:02:35 -0600;
  • 8ed712b v1.2.3 -- update to latest biocthis GHA; replace knitcitations with RefManageR by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-18 13:17:48 -0500;
  • 796bc64 v1.3.3 -- update to latest biocthis GHA; replace knitcitations with RefManageR by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-18 13:17:48 -0500;
  • f263371 upgrade regutools version 1.3.1 -> 1.3.2 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-12-07 02:20:58 -0600;
  • 082357f upgrade version of regulondb 10.6 -> 10.8 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-12-07 02:02:35 -0600;
  • 5330c34 v1.3.1 -- merge with Bioc's git. b36cba5 should have been v1.3.1. by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-11-25 15:12:53 -0500;
  • 4cde8a3 v1.2.1 -- Match the devel branch from b36cba5 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-11-25 15:08:23 -0500;
  • b36cba5 v1.1.4 -- switch to the latest biocthis GHA workflow. Update URL to resolve https://github.com/ComunidadBioInfo/regutools/issues/33 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-11-25 15:08:23 -0500;
  • 71d3f49 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 11:56:52 -0400;
  • d0e6ed5 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 11:56:52 -0400;
  • 2ff109f update date version by Joselyn Chavez <joselynchavezf@gmail.com> 2020-10-11 18:13:51 -0500;
  • a5107d3 update Version 1.1.2 -> 1.1.3 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-10-11 14:24:07 -0500;
  • d7820f0 add NEWS for version 1.1.3 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-10-11 14:23:36 -0500;
  • 7732515 updated bioRxiv -> Bioinformatics citation by Joselyn Chavez <joselynchavezf@gmail.com> 2020-10-11 14:23:04 -0500;
  • c72f8ec update roxygen version by Joselyn Chavez <joselynchavezf@gmail.com> 2020-10-10 15:36:47 -0500;
  • 4c5868f update documentation due to roxygen update by Joselyn Chavez <joselynchavezf@gmail.com> 2020-10-10 15:36:37 -0500;
  • 9815ff9 mcols() -> GenomicRanges::mcols() by Joselyn Chavez <joselynchavezf@gmail.com> 2020-10-10 15:30:53 -0500;
  • 7a67896 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-05-27 01:10:37 -0400;
  • 7ebbd55 Adding the latest dev files from https://github.com/lcolladotor/biocthis/commit/61e65ee854aff39d7c90f3df72ab842b77a15d10 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-05-10 12:17:31 -0400;
  • a2d95a6 v1.1.2 -- Update to match https://github.com/lcolladotor/biocthis/commit/61e65ee854aff39d7c90f3df72ab842b77a15d10 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-05-10 11:37:48 -0400;
  • 09bf04e (origin/RELEASE_3_11, RELEASE_3_11) v1.0.1 -- update CITATION. Now also use biocthis::use_bioc_pkg_templates() for the /dev templates by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-30 13:54:47 -0400;
  • c6d2df5 v1.1.1 -- update CITATION. Now also use biocthis::use_bioc_pkg_templates() for the /dev templates by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-30 13:54:47 -0400;
  • 281285f 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 19:36:28 +0000;
  • ee1222e 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 19:36:28 +0000;
  • 1f2b65f Update to match https://github.com/leekgroup/derfinderPlot/commit/4124541 /nocache by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-27 10:17:50 -0400;
  • d6c44d0 Update to match https://github.com/leekgroup/derfinderPlot/commit/8695cbe /nocache by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 23:34:09 -0400;
  • d229edc Update to match https://github.com/leekgroup/derfinderPlot/commit/bae121d by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-25 20:07:19 -0400;
  • 6551e75 v0.99.15 -- bump version as promised in https://github.com/Bioconductor/Contributions/issues/1393#issuecomment-617471293 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 23:48:04 -0400;
  • 8d9e4f9 v0.99.14 -- update the arguments and help page for connect_database() now that we are using BiocFileCache by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 19:26:11 -0400;
  • c50700a v0.99.13 -- Use BiocFileCache for caching the db when it's downloaded from Dropbox instead of AnnotationHub by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 19:00:23 -0400;
  • 629aecd Update README.md by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 18:40:40 -0400;
  • 4f1c9d5 Add files missing in the previous commit by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 18:37:59 -0400;
  • d254e8a v0.99.12 -- Switch to GitHub actions as described in https://github.com/r-lib/actions/issues/84 using the GHA workflow from https://github.com/leekgroup/derfinderPlot/commit/83990df364c94859df7e81e5c13bc8311f7d285e by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 18:37:40 -0400;
  • 2b72973 version bump to 0.99.11 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-13 17:57:45 -0500;
  • ae9f271 add description for version 0.99.11 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-13 17:56:10 -0500;
  • dca65a0 manual adjustment for lines > 80 chr in params description by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-13 17:55:55 -0500;
  • d8a9bbf add description for version 0.99.11 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-13 17:54:43 -0500;
  • 5686d33 bump to version 0.99.10 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-13 14:13:07 -0500;
  • add3846 bump to version 0.99.9 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-08 22:49:25 -0500;
  • 7fdd198 Add NEWS for version 0.99.9 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-08 19:01:03 -0500;
  • ceb9a44 Add suggested biocView Transcription by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-08 18:59:39 -0500;
  • ba77100 v0.99.8 -- Change biocViews by Car BarJon <car.barjon@gmail.com> 2020-04-07 17:50:40 -0700;
  • a990fbc v0.99.7 -- fix pkgdown deployment based on the solution presented at https://github.com/r-lib/pkgdown/pull/1276 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-07 20:30:44 -0400;
  • 8497185 bump version to 0.99.6 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-07 16:11:30 -0500;
  • d70e283 NEWS added for version 0.99.6 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-07 15:48:02 -0500;
  • ea5396f manual adjustment for lines > 80 chr using paste() by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-07 13:28:29 -0500;
  • 209d5e7 manual adjustment to 80 character lines by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-07 01:39:58 -0500;
  • fbb21bd manual adjustment for multiples of 4 characters by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-07 00:54:04 -0500;
  • 05eb391 bump to version 0.99.5 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-06 23:14:48 -0500;
  • fa9f1ac Update NEWS for version 0.99.5 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-06 23:13:53 -0500;
  • 4452362 Reindent lines by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-06 22:54:27 -0500;
  • 4108931 version updated to 0.99.4 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-06 14:32:49 -0500;
  • 73e65d7 spaces adjusted to multiples of 4 spaces by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-06 14:18:55 -0500;
  • 2241964 lines adjusted to 80 characters by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-06 14:12:55 -0500;
  • 30d5b2c back to original line 85 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-05 19:26:14 -0500;
  • fe6cf12 back to original line 106 to evaluate package building by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-04 21:35:31 -0600;
  • d424d78 adjust lines to 80 characters by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-04 15:30:42 -0600;
  • 0562fc6 add news for version 0.99.3 and 0.99.4, modified news for 0.99.0 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-04-04 15:29:57 -0600;
  • 78393d9 update package version to 0.99.3 by Joselyn Chavez <joselynchavezf@gmail.com> 2020-03-16 14:37:46 -0600;
  • c83d194 update package Description by Joselyn Chavez <joselynchavezf@gmail.com> 2020-03-16 14:34:22 -0600;
  • f5a28b0 fix bug with Cytoscape conection by setting visual parameters manually by Joselyn Chavez <joselynchavezf@gmail.com> 2020-03-16 14:32:54 -0600;
  • 8e1c802 update Description with an article-like summary by Joselyn Chavez <joselynchavezf@gmail.com> 2020-03-16 14:30:12 -0600;
  • 5a77624 v0.99.2 -- remove the .Rproj file :'( and bumped R depends to 4.0 (might break) by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-03-03 13:55:59 -0500;
  • 957be1c Removed the Rproj file =( by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-03-03 13:49:50 -0500;
  • 16da039 v0.99.1 -- address as many issues from http://bioconductor.org/spb_reports/regutools_buildreport_20200302121040.html#malbec2_check_anchor except the BiocCheck warning about R 4.0. Bump version with all recent changes by the rest of the team as well. by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-03-03 13:01:30 -0500;
  • 58ab35e short example line width by Joselyn Chavez <joselynchavezf@gmail.com> 2020-03-02 22:39:47 -0600;
  • dc67445 Add value information for - [x] man/convert_to_biostrings.Rd - [x] man/convert_to_granges.Rd, - [x] man/guess_id.Rd, - [x] man/list_datasets.Rd, by Car BarJon <car.barjon@gmail.com> 2020-03-02 21:51:40 -0600;
  • e1440e8 Addressed 3 of the BiocCheck warnings by areyesq89 <alejandro.reyes.ds@gmail.com> 2020-03-02 17:29:20 -0500;
  • 0cb5b18 Fix citation info (biorxiv template) but also somehow re-add stuff that was broken by https://github.com/ComunidadBioInfo/regutools/commit/3192f1590fe73c82eeb42b160cee5efdfc392107 (dunno how that happened) by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-02-29 15:19:35 -0500;
  • c12b3f1 fix R CMD check by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-02-29 12:42:49 -0500;
  • 3192f15 Update READMEs, citation info by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-02-29 12:38:17 -0500;
  • d163790 add logo by Car BarJon <car.barjon@gmail.com> 2020-02-29 11:14:51 -0600;
  • d3538de vignette updated to show get_dna_objects and plot_dna_objects in action by Joselyn Chavez <joselynchavezf@gmail.com> 2020-02-28 23:05:19 -0600;
  • 3850add change parameters 'from' and 'to' to grange by Joselyn Chavez <joselynchavezf@gmail.com> 2020-02-28 21:38:04 -0600;
  • bde5d28 add expect_error when non-valid GRanges are provided by Joselyn Chavez <joselynchavezf@gmail.com> 2020-02-28 21:37:30 -0600;
  • fab452c remove previous range validation by Joselyn Chavez <joselynchavezf@gmail.com> 2020-02-28 21:27:52 -0600;
  • a2a98fa remove data.table from bib in vignette by Joselyn Chavez <joselynchavezf@gmail.com> 2020-02-28 21:24:20 -0600;
  • c3ab8ab Add explicit IRanges::IRanges by Joselyn Chavez <joselynchavezf@gmail.com> 2020-02-28 21:04:04 -0600;
  • 6605bc9 explicit declare GenomicRanges::GRanges by Joselyn Chavez <joselynchavezf@gmail.com> 2020-02-28 20:50:15 -0600;