1. MIRA
  2. Graph
Graph of MIRA
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  • 0582ff6 (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 11:00:09 -0400;
  • a6d3f7c (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 11:00:09 -0400;
  • 33b1d13 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 10:56:59 -0400;
  • 405695d (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 10:56:59 -0400;
  • e528412 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 11:16:28 -0400;
  • 167d3f7 (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 11:16:28 -0400;
  • b1a330f 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 15:43:48 +0000;
  • 297ceb8 (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 15:43:48 +0000;
  • f4b7c2e Pass serialized S4 instances thru updateObject() by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-21 00:34:23 -0500;
  • 319b115 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 16:38:36 +0000;
  • 40eceb4 (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 16:38:36 +0000;
  • 6ac4523 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 16:30:47 +0000;
  • ac36885 (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 16:30:47 +0000;
  • 06ca830 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 11:28:13 -0400;
  • c1a0840 (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 11:28:13 -0400;
  • 696479f 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 19:10:54 +0000;
  • d1bdf22 (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 19:10:54 +0000;
  • 1c66f4f Version bump by U-John-PC\John L <7jlawson@gmail.com> 2020-04-09 15:18:35 -0400;
  • ef41e92 Remove path that caused error by U-John-PC\John L <7jlawson@gmail.com> 2020-04-08 11:06:37 -0400;
  • 3b5317f 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 13:42:29 -0400;
  • eb5b6ae (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 13:10:48 -0400;
  • 930be3b Small updates by U-John-PC\John L <7jlawson@gmail.com> 2019-10-24 16:47:14 -0400;
  • e1322a2 Merge branch 'dev' of github.com:databio/MIRA by U-John-PC\John L <7jlawson@gmail.com> 2019-10-24 16:11:22 -0400;
  • cb48f63 Warning if differing region sizes in the same region set given to aggregateMethyl() by U-John-PC\John L <7jlawson@gmail.com> 2017-10-30 23:15:09 -0400;
  • 1f4f22f standardize style by nsheff <nsheff@users.noreply.github.com> 2019-06-10 16:31:33 -0400;
  • e5e8d1d 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 12:15:13 -0400;
  • e4c8897 (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 11:54:09 -0400;
  • 651d1fa Update DESCRIPTION by Nathan Sheffield <nsheff@users.noreply.github.com> 2019-03-21 12:35:10 -0400;
  • 1986619 (origin/RELEASE_3_8, RELEASE_3_8) Add ImmunoOncology biocViews term by Kayla-Morrell <kayla.morrell@roswellpark.org> 2019-01-04 13:15:24 -0500;
  • 1cdde35 Add ImmunoOncology biocViews term by Kayla-Morrell <kayla.morrell@roswellpark.org> 2019-01-04 13:15:20 -0500;
  • 974cb69 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:38 -0400;
  • 33171ef bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:42:06 -0400;
  • 278447d Version bump for new build by U-John-PC\John L <7jlawson@gmail.com> 2018-10-24 23:32:17 -0400;
  • 432c0a5 Merge branch 'master' of git.bioconductor.org:packages/MIRA by U-John-PC\John L <7jlawson@gmail.com> 2018-10-24 23:26:59 -0400;
  • 4b7a27a Fix check and bioccheck note/warning by U-John-PC\John L <7jlawson@gmail.com> 2018-10-24 23:26:32 -0400;
  • 6dfff55 plotMIRAProfiles: make name for sample type column flexible by U-John-PC\John L <7jlawson@gmail.com> 2018-10-24 22:58:44 -0400;
  • 7a9a120 Update reference, remove legend for plotMIRAprofiles if only one or no sampleType given by U-John-PC\John L <7jlawson@gmail.com> 2018-10-24 13:39:18 -0400;
  • 4dc2b67 Fix format of NEWS by U-John-PC\John L <7jlawson@gmail.com> 2018-10-20 20:40:13 -0400;
  • feec689 Merge pull request <a href="#24">#24</a> from databio/master by John Lawson <j-lawson@users.noreply.github.com> 2018-10-20 20:27:14 -0400;
  • d884d67 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:43 -0400;
  • 99bbed2 (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 10:35:48 -0400;
  • a283975 bump version from invalid version to valid by vobencha <valerie.obenchain@roswellpark.org> 2018-04-26 18:59:21 -0700;
  • eda23b7 Test against R devel with Travis CI by U-John-PC\John L <7jlawson@gmail.com> 2018-04-20 12:55:46 -0400;
  • a1fabf3 Reduce size of data files and update suggests/enhances by U-John-PC\John L <7jlawson@gmail.com> 2018-04-20 12:40:38 -0400;
  • 4c24c6d Version bump after bug fix by U-John-PC\John L <7jlawson@gmail.com> 2018-04-17 15:19:26 -0400;
  • 56b1bcf Bug fix: Update BSseq object to work with new Bioconductor release by U-John-PC\John L <7jlawson@gmail.com> 2018-04-16 20:35:46 -0400;
  • 4eaaca9 Fix typo by U-John-PC\John L <7jlawson@gmail.com> 2018-04-10 17:53:59 -0400;
  • 3169326 Update NEWS, version bump by U-John-PC\John L <7jlawson@gmail.com> 2018-04-10 17:35:49 -0400;
  • ece3776 Bug fix: fix instance when no regions from region set overlap with sample, also add new warnings and tests by U-John-PC\John L <7jlawson@gmail.com> 2018-04-10 14:28:47 -0400;
  • be8fe96 Doc updates: version bump by U-John-PC\John L <7jlawson@gmail.com> 2017-11-02 23:48:31 -0400;
  • 2c05d10 (origin/RELEASE_3_6, RELEASE_3_6) Version bump (and switching to even y in x.y.z) by John Lawson <j-lawson@users.noreply.github.com> 2017-11-02 23:31:41 -0400;
  • e55c7dc Merge pull request <a href="#23">#23</a> from databio/doc_updates by John Lawson <j-lawson@users.noreply.github.com> 2017-11-02 23:17:15 -0400;
  • 15db3e5 Adding sample code/section for LOLA to getting started vignette by U-John-PC\John L <7jlawson@gmail.com> 2017-11-02 22:40:31 -0400;
  • 2626663 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:54:33 -0400;
  • 86db421 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 12:41:58 -0400;
  • 6d12c2b Merge pull request <a href="#22">#22</a> from databio/dev by John Lawson <j-lawson@users.noreply.github.com> 2017-10-28 17:26:40 -0400;
  • 23dc656 Version bump and documentation updates by U-John-PC\John L <7jlawson@gmail.com> 2017-10-28 17:01:43 -0400;
  • e9b4ec4 Clarification about consistent region sizes and update example syntax by U-John-PC\John L <7jlawson@gmail.com> 2017-10-28 10:54:36 -0400;
  • b08cc7a Catching up documentation and version bump by U-John-PC\John L <7jlawson@gmail.com> 2017-10-27 12:24:48 -0400;
  • 9bee3fa Adding section on statistical test to BiologicalApplication vignette by U-John-PC\John L <7jlawson@gmail.com> 2017-10-27 10:02:37 -0400;
  • 3da87de Updates to Getting Started vignette by U-John-PC\John L <7jlawson@gmail.com> 2017-10-26 16:01:00 -0400;
  • ef11595 Documentation updates by U-John-PC\John L <7jlawson@gmail.com> 2017-10-26 13:15:00 -0400;
  • 2e2f95a Updates to NEWS file by U-John-PC\John L <7jlawson@gmail.com> 2017-10-24 13:20:55 -0400;
  • c8d5e93 Merge pull request <a href="#21">#21</a> from databio/dev by John Lawson <j-lawson@users.noreply.github.com> 2017-10-22 13:24:34 -0400;
  • 3f94a4b Update citation and version bump by U-John-PC\John L <7jlawson@gmail.com> 2017-10-22 13:14:22 -0400;
  • a783f8b BSreadBiseq no longer adds sampleName col, MIRAScore wrapper function is no longer exported because user should use aggregateMethyl and calcMIRAScore instead by U-John-PC\John L <7jlawson@gmail.com> 2017-10-21 15:59:55 -0400;
  • 394da35 Documentation updates by U-John-PC\John L <7jlawson@gmail.com> 2017-10-21 13:36:29 -0400;
  • 18fd901 Merge pull request <a href="#20">#20</a> from databio/dev by John Lawson <j-lawson@users.noreply.github.com> 2017-10-17 16:42:28 -0400;
  • 390e3bd Version bump by U-John-PC\John L <7jlawson@gmail.com> 2017-10-17 16:15:02 -0400;
  • 646505b Bug fix: fixing coverage name in tests by U-John-PC\John L <7jlawson@gmail.com> 2017-10-17 15:33:06 -0400;
  • c9a78de Bug fix: bug introduced by change to buildJ/name change of coverage => sumCoverage by U-John-PC\John L <7jlawson@gmail.com> 2017-10-17 15:16:20 -0400;
  • 76d8010 Change names: scoreDip => calcMIRAScore, scoreDipInt => scoreDip. calcMIRAScore is now the name of the main scoring function that will be used in vignettes and by the user by U-John-PC\John L <7jlawson@gmail.com> 2017-10-17 11:27:37 -0400;
  • 53f324e Changed output coverage col to sumCoverage to be more clear that it is not quite the same type of thing as input coverage by U-John-PC\John L <7jlawson@gmail.com> 2017-10-17 10:41:19 -0400;
  • e4f9fd7 Changing minReads parameter name to minBaseCovPerBin for increased clarity by U-John-PC\John L <7jlawson@gmail.com> 2017-10-16 22:44:59 -0400;
  • c93783d Merge remote-tracking branch 'upstream/master' into dev by U-John-PC\John L <7jlawson@gmail.com> 2017-10-16 21:50:38 -0400;
  • f632710 Major change: sampleName column not needed/added during aggregation step to save memory by U-John-PC\John L <7jlawson@gmail.com> 2017-10-16 21:39:09 -0400;
  • 564c2b4 Adding is() function to namespace by John Lawson <j-lawson@users.noreply.github.com> 2017-10-02 15:45:53 -0400;
  • 7cc99c4 Bump version number for new Bioc build by j-lawson <jtl2hk@virginia.edu> 2017-10-02 15:44:39 -0400;
  • 34bcfb7 Adding is() function to namespace by j-lawson <jtl2hk@virginia.edu> 2017-10-02 15:30:26 -0400;
  • e70e588 Updating package based on additional comments from Herve by John Lawson <j-lawson@users.noreply.github.com> 2017-10-02 14:58:50 -0400;
  • 4dbc282 Fix bug about trying to test multiple classes with one is() statement by j-lawson <jtl2hk@virginia.edu> 2017-10-02 14:41:12 -0400;
  • 67cf59e Version bump for new Bioconductor build by j-lawson <jtl2hk@virginia.edu> 2017-10-02 14:21:03 -0400;
  • e2a014e Replacing (object %in% class) syntax with is(object, class) to prevent bugs by j-lawson <jtl2hk@virginia.edu> 2017-10-02 14:17:38 -0400;
  • 363c47e Adding titles to the data documentation by j-lawson <jtl2hk@virginia.edu> 2017-10-02 13:10:41 -0400;
  • eb3ea1e Using <- for assignment instead of = by j-lawson <jtl2hk@virginia.edu> 2017-10-02 12:29:29 -0400;
  • 491cdff Update .Rd file by U-John-PC\John L <7jlawson@gmail.com> 2017-09-21 14:06:52 -0400;
  • a413117 Fix documentation format by John Lawson <j-lawson@users.noreply.github.com> 2017-09-21 13:52:06 -0400;
  • c1edeee Fixing MIRA title for documentation website by John Lawson <j-lawson@users.noreply.github.com> 2017-09-20 19:00:33 -0400;
  • a8a5bf8 Significant updates to user interface and documentation by John Lawson <j-lawson@users.noreply.github.com> 2017-09-08 17:42:17 -0400;
  • 59c0f09 Merge branch 'master' into dev by John Lawson <j-lawson@users.noreply.github.com> 2017-09-08 17:38:20 -0400;
  • d1a33e3 Version bump for Bioc build by John Lawson <j-lawson@users.noreply.github.com> 2017-09-08 17:34:14 -0400;
  • 7590a65 Small format/documentation changes by j-lawson <jtl2hk@virginia.edu> 2017-09-08 16:48:35 -0400;
  • 61925df Taking out 0 step from list to prevent confusion by John Lawson <j-lawson@users.noreply.github.com> 2017-09-08 13:47:29 -0400;
  • 744f5c3 add whitespace so list renders correctly by nsheff <nathan@code.databio.org> 2017-09-07 21:59:55 -0400;
  • 01c3bab asterisk lists to hyphen for HTML output by nsheff <nathan@code.databio.org> 2017-09-07 21:01:21 -0400;
  • 051e682 Fix readme whitespace by nsheff <nathan@code.databio.org> 2017-09-07 21:00:20 -0400;
  • d9c0d3e add pkgdown config by nsheff <nathan@code.databio.org> 2017-09-07 20:45:20 -0400;
  • bd05303 Fixing tests after updates to scoreDip() and updating documentation by j-lawson <jtl2hk@virginia.edu> 2017-09-05 10:23:51 -0400;
  • 46ebfac Change to user interface for scoreDip(). It now takes a data.table as input but it can be run with normal R syntax instead of requiring data.table syntax (being used in the j expression) by U-John-PC\John L <7jlawson@gmail.com> 2017-09-05 09:40:12 -0400;
  • 6a52926 Changing function call in vignette to reflect not needing binCount parameter. Updating NEWS by U-John-PC\John L <7jlawson@gmail.com> 2017-08-31 20:05:14 -0400;