1. MotifDb
  2. Graph
Graph of MotifDb
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  • 625db80 (HEAD -> devel, origin/devel, origin/HEAD) bumped version by paul-shannon <paul.thurmond.shannon@gmail.com> 2025-03-12 13:35:46 -0700;
  • a947ca2 default target, tests now accomodate jaspar2024 and hocomocov13 by paul-shannon <paul.thurmond.shannon@gmail.com> 2025-03-12 13:35:14 -0700;
  • d040621 updates to jaspar and hocomoco by paul-shannon <paul.thurmond.shannon@gmail.com> 2025-03-12 12:50:00 -0700;
  • 5d68529 updates to jaspar and hocomoco by paul-shannon <paul.thurmond.shannon@gmail.com> 2025-03-12 12:49:31 -0700;
  • bfe94e0 new updates from jaspar and hocomoco by paul-shannon <paul.thurmond.shannon@gmail.com> 2025-03-12 12:39:34 -0700;
  • c4cd303 (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 09:42:14 -0400;
  • 02ccdc9 (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 09:42:14 -0400;
  • eff8f41 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 10:28:32 -0400;
  • 612f541 (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 10:28:32 -0400;
  • 3a552ea 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 09:50:54 -0400;
  • 12d072e (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 09:50:54 -0400;
  • 4e2e1f8 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 10:23:46 -0400;
  • 1b9f24c (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 10:23:46 -0400;
  • 113732b 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 11:07:15 -0400;
  • 213f1a8 (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 11:07:15 -0400;
  • b83abe4 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 15:11:46 +0000;
  • d45f2bf (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 15:11:45 +0000;
  • 4de1d63 merge by paul-shannon <paul.thurmond.shannon@gmail.com> 2022-03-23 14:48:50 -0700;
  • 5b92878 updated show method, renamed to makefile by paul-shannon <paul.thurmond.shannon@gmail.com> 2022-03-04 13:16:37 -0800;
  • 01b1ed7 legal version bump by paul-shannon <paul.thurmond.shannon@gmail.com> 2022-03-04 12:49:59 -0800;
  • d5a8a2d jaspar2022 added by paul-shannon <paul.thurmond.shannon@gmail.com> 2022-03-04 12:48:22 -0800;
  • dc2076d 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 16:04:11 +0000;
  • 7e45029 (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 16:04:11 +0000;
  • 67a8189 full version restored by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-10-03 08:49:33 -0700;
  • 8feeb4a fixed onload error, moved tfs RData file to tfs directory by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-10-03 08:37:53 -0700;
  • 35338ce merge by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-09-21 15:54:53 -0700;
  • 9d696e1 format error in letter-probablity matrix fixed by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-09-21 15:54:33 -0700;
  • a79349e for reference: TFs w/ and w/o motifs by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-09-21 15:53:01 -0700;
  • 3fc5bd6 suggests markdown by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-09-01 10:30:30 -0700;
  • fd88b87 bumped version number by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-08-25 11:01:30 -0700;
  • 5b27be4 removed all mention of markdown package by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-08-25 10:49:02 -0700;
  • d5cce9f fixed knitr error by paul-shannon <paul.thurmond.shannon@gmail.com> 2021-08-23 08:17:04 -0700;
  • 97ed561 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 15:53:25 +0000;
  • ed81ab9 (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 15:53:25 +0000;
  • 0e13afe 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 10:46:46 -0400;
  • 99f1d5a (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 10:46:46 -0400;
  • 1aef8fe 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 18:30:46 +0000;
  • 760cd7e (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 18:30:46 +0000;
  • 1a97e0d knitr now SUGGESTED by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-21 07:40:19 -0700;
  • 1a90fb1 bumped version to catch new knitr vignette, updated NEWS by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-14 09:58:57 -0700;
  • 59957bc new knitr vignette by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-14 09:54:50 -0700;
  • 7a1d7a8 more sections added by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-10 08:46:50 -0700;
  • 27edd92 quick start section added by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-09 08:37:49 -0700;
  • 39230c1 work in progress: shifting from Sweave to knitr by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-07 10:40:05 -0700;
  • 8cc16fa removed MotIV from suggests by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-04 11:02:19 -0700;
  • 28a9214 removed MotIV from unitTests by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-04 10:59:55 -0700;
  • a3aca6d removed motifmatchr and its dependencies by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-04-02 13:20:03 -0700;
  • 2d7af58 hocomoco core|secondary names now used for matrices & rownames mcols by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-03-18 13:22:29 -0700;
  • fe1bab0 non-core hocomocov11 motifs tagged 'full' now 'secondary' by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-03-18 12:22:54 -0700;
  • f56272b hocomoco v11 can be queried by core|full and reliability (A-D) by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-03-16 16:36:31 -0700;
  • 62c3f77 fixed version number by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-03-09 17:09:45 -0700;
  • 5b88116 provisional addition of hocomoco v1, with reliability scores, A-D by paul-shannon <paul.thurmond.shannon@gmail.com> 2020-03-09 17:06:57 -0700;
  • 04ce14e 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 13:36:20 -0400;
  • 3602d2b (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 13:08:33 -0400;
  • 44df9f7 merge by paul-shannon <paul.thurmond.shannon@gmail.com> 2019-05-06 11:53:08 -0700;
  • 5c623f6 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 12:11:14 -0400;
  • e3f6e55 (origin/RELEASE_3_9, RELEASE_3_9) 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 11:53:37 -0400;
  • db0caa6 (origin/RELEASE_3_8, RELEASE_3_8) bumped version number by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-11-06 05:50:08 -0800;
  • de8673a R requirement backed off from 3.5.1 to 3.5.0 by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-11-03 12:23:56 -0700;
  • ba1149f depends now on R 3.5.0, not 3.5.1 by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-11-03 12:21:49 -0700;
  • f118237 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:30 -0400;
  • dde54cd bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:49 -0400;
  • 5da060a improved docs for query method by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-10-24 12:02:56 -0700;
  • d8e8261 merged DESCRIPTION file by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-10-18 07:20:52 -0700;
  • 4b66948 big speedup of associateTranscriptionFactors method, exploiting duplicate motifs by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-10-18 07:18:37 -0700;
  • f394b40 merge by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-08-17 09:54:43 -0700;
  • 42f0181 added explicit return from plotMotifs by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-08-17 09:54:08 -0700;
  • 7a60c91 removed depends motifStack by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-07-07 12:33:31 -0700;
  • 48c3af4 motif/tf mapping now includes the 'both' option, tfclass and motifdb. motifStack plotting added by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-06-03 11:31:01 -0700;
  • 9535d30 motifToGene fix: now combined empty source table with populated table by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-05-23 11:32:17 -0700;
  • fda2dea associateTranscriptionFactors greatly simplified, builds upon motifToGene by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-05-18 16:22:10 -0700;
  • aaf4e1a motifToGene refactored, now suuports c('motifDb', tfClass') sources by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-05-18 15:05:19 -0700;
  • 3cb31fd added query2(mdb, andTerms, orTerms=c(), notTerms=c()) by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-05-10 16:52:12 -0700;
  • d8d41e7 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:39 -0400;
  • 63accd6 (origin/RELEASE_3_7, RELEASE_3_7) bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:35:26 -0400;
  • 388ccbc added cisbp 2014 reference by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-04-08 22:47:55 -0700;
  • 2d366f4 merged by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-02-01 16:07:35 -0800;
  • 68ba7eb motifToGene and geneToMotif now guard against emtpy tables, ignore.cae option added by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-02-01 16:04:51 -0800;
  • e2f7996 removed test_Imports.R, pkg passes CHECK by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-01-23 10:14:17 -0800;
  • 5f111ac added unit test to clarify geneToMotif results by paul-shannon <paul.thurmond.shannon@gmail.com> 2018-01-23 08:54:36 -0800;
  • b7a40ef Added jaspar 2018 by Matthew Richards <mrichard@buoy.systemsbiology.net> 2017-12-07 18:17:22 -0800;
  • f03d3fc bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:22 -0400;
  • 704c856 (origin/RELEASE_3_6, RELEASE_3_6) bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:39:49 -0400;
  • b6c129a Fixed labeling of cisbp motifs by Matthew Richards <mrichard@buoy.systemsbiology.net> 2017-10-20 13:45:38 -0700;
  • 31071c4 updated for release by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-13 09:41:24 -0700;
  • dae43ec noted query problem, with embedded regex chars by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-08 09:38:03 -0700;
  • 8c4dd89 Removed large text files by Matthew Richards <mrichard@buoy.systemsbiology.net> 2017-10-04 15:42:47 -0700;
  • 07b8ea8 string comparisons now sorted by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-04 15:35:57 -0700;
  • 1157d7e merged by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-04 15:21:26 -0700;
  • 1ae931f tracking down motif name equality bug by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-04 15:07:08 -0700;
  • e90f526 getlocale in failing test by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-04 14:10:45 -0700;
  • 4acf0d7 documentation for geneToMotif, motifToGene, associateT... by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-04 12:49:25 -0700;
  • bca83fc bumped version by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-04 10:49:50 -0700;
  • 0aa3bd2 lexical only: renamed 2 variables by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-04 10:49:04 -0700;
  • d030e74 motifToGene sidesteps regexes by grep fixed=TRUE by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-10-03 11:13:41 -0700;
  • b7fe234 Removed large text files by Matthew Richards <mrichard@buoy.systemsbiology.net> 2017-10-03 09:42:17 -0700;
  • 3b614ce motif/TF mapping sources now case insensitive by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-09-26 13:09:39 -0700;
  • 1f060cb Fixed jaspar format spacing and updated DESCRIPTION by Matthew Richards <mrichard@buoy.systemsbiology.net> 2017-09-18 11:31:33 -0700;
  • 094b985 now annotates to TFs properly for MotifDb and TFClass sources by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-09-12 13:20:46 -0700;
  • 49ebd9d geneToMotif, motifToGene, associateTranscriptionFactors tested by paul-shannon <paul.thurmond.shannon@gmail.com> 2017-09-07 16:28:23 -0700;