Graph ofCoGAPS
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  • ace4b90f2 (HEAD -> master, origin/master, origin/HEAD) 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 15:05:27 +0000;
  • 64e95afe6 (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 15:05:27 +0000;
  • 79a489ffb beware the ides of march by jeanettejohnson <johnsonje197@gmail.com> 2022-03-15 18:11:04 -0400;
  • 3ac821e3d increment version by jeanettejohnson <johnsonje197@gmail.com> 2022-03-15 17:41:56 -0400;
  • ce08c64c9 Update class-CogapsResult.R by Jeanette Johnson <jjohn450@jhmi.edu> 2022-03-01 14:40:40 -0500;
  • 917dcab8e Update DESCRIPTION by Elana J Fertig <ejfertig@jhmi.edu> 2022-01-13 17:20:04 -0500;
  • a8fb99918 Merge pull request <a href="#60">#60</a> from FertigLab/pattern-markers-fix by Jeanette Johnson <jjohn450@jhmi.edu> 2022-01-06 16:04:22 -0500;
  • a22125534 fix thresholding by Davin Brownell <davin@Davins-MacBook-Pro.local> 2022-01-06 16:01:42 -0500;
  • d2cd8a1c4 Create DFrame instance in place of a DataFrame instance by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-21 03:15:49 -0800;
  • 64fb0ba97 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 15:56:36 +0000;
  • f937a7c3c (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 15:56:36 +0000;
  • 206bac963 Merge pull request <a href="#57">#57</a> from FertigLab/plot-pattern-markers-fix by Jeanette Johnson <jjohn450@jhmi.edu> 2021-10-19 14:33:03 -0400;
  • b71d5c7b4 Merge pull request <a href="#59">#59</a> from FertigLab/plot-result-by-group by Jeanette Johnson <jjohn450@jhmi.edu> 2021-10-19 13:25:14 -0400;
  • 335005b10 oops left in a hardcoded number by jeanettejohnson <johnsonje197@gmail.com> 2021-10-15 16:44:13 -0400;
  • 8b3a0715d basic plot function takes optional groups param for large datasets by jeanettejohnson <johnsonje197@gmail.com> 2021-10-15 16:08:28 -0400;
  • e1e002caa Update GapsResult.h by Jeanette Johnson <jjohn450@jhmi.edu> 2021-10-05 18:20:56 -0400;
  • 86cb3fee9 not broken by Jeanette Johnson <jjohn450@jhmi.edu> 2021-10-05 18:20:12 -0400;
  • 5308f8964 not broken by Jeanette Johnson <jjohn450@jhmi.edu> 2021-10-05 18:19:16 -0400;
  • 93aec7aa3 not broken by Jeanette Johnson <jjohn450@jhmi.edu> 2021-10-05 18:18:43 -0400;
  • 933588d34 plot pattern amp by group by Jeanette Johnson <johnsonje197@gmail.com> 2021-10-05 17:21:40 -0400;
  • e494cf3ac empty constructors for python bindings by Jeanette Johnson <johnsonje197@gmail.com> 2021-10-05 17:03:24 -0400;
  • 10124fa8a Merge pull request <a href="#58">#58</a> from FertigLab/0add1d9995 by Jeanette Johnson <jjohn450@jhmi.edu> 2021-08-18 15:53:41 -0400;
  • 73c485b85 tiny change to cogaps so it compiles by Jeanette Johnson <johnsonje197@gmail.com> 2021-08-17 15:37:49 -0400;
  • e5ae91adf fixed plotPatternMarkers function? by Jeanette Johnson <johnsonje197@gmail.com> 2021-07-21 13:10:33 -0400;
  • 2369fe559 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 15:45:58 +0000;
  • c297d7ea5 (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 15:45:58 +0000;
  • 8e52cf680 Using -march=native on Windows should not be needed by Hervé Pagès <hpages.on.github@gmail.com> 2020-12-30 17:47:01 -0800;
  • e448a5906 Fixed merge conflict by lothm2014 <lothm2014@yahoo.com> 2020-11-23 07:49:16 -0500;
  • 898e0728f Updated version on README by lothm2014 <lothm2014@yahoo.com> 2020-11-23 07:43:57 -0500;
  • 04046b9db Updated version on bh updates by lothm2014 <lothm2014@yahoo.com> 2020-11-23 07:42:06 -0500;
  • ffe8aca25 upped version of description by ejfertig <ejfertig@jhmi.edu> 2020-10-29 15:07:11 -0400;
  • c7bfef9db added BH dependency by ejfertig <ejfertig@jhmi.edu> 2020-10-29 15:01:56 -0400;
  • f34ce7ea3 remove manual inclusion of boost by ejfertig <ejfertig@jhmi.edu> 2020-10-29 14:53:48 -0400;
  • 4670e247c 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 10:38:41 -0400;
  • 395fcd3b9 (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 10:38:41 -0400;
  • 0add1d999 Version bump by sherman5 <tomsherman159@gmail.com> 2020-10-20 00:06:19 -0400;
  • f0d19bb06 Disable SIMD for MinGW by sherman5 <tomsherman159@gmail.com> 2020-10-20 00:06:00 -0400;
  • 65e6c61f9 Version bump by sherman5 <tomsherman159@gmail.com> 2020-10-19 23:47:46 -0400;
  • 0e6c418d0 Disable hand-rolled SIMD on Windows by sherman5 <tomsherman159@gmail.com> 2020-10-19 23:45:47 -0400;
  • 2fb5c7b0c Merge branch 'upstream/master' into develop by lothm2014 <lothm2014@yahoo.com> 2020-10-16 11:36:18 -0400;
  • 5be3812b9 Merge pull request <a href="#53">#53</a> from lothm2014/develop by genesofeve <gsteinobrien@gmail.com> 2020-10-16 09:50:36 -0400;
  • 12f2dc45f Updated license to BSD_3_clause + file LICENSE by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 19:05:20 -0400;
  • 68df09958 Update license to BSD-3 by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 18:37:12 -0400;
  • 96ed169f6 Fixed license name by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 17:54:16 -0400;
  • d79f30662 Update ChangeLog by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 15:18:37 -0400;
  • 2594de941 Updated version in README by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 15:16:54 -0400;
  • 2fa936fd5 Updated version number in description by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 15:16:27 -0400;
  • b9d530b24 Updated license in DESCRIPTION by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 15:15:51 -0400;
  • c795c324b Added Melanie to maintainer by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 15:15:12 -0400;
  • 707a6dd08 Delete COPYING by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 15:14:26 -0400;
  • b2727d12f Added BSD License by Melanie Loth <59892258+lothm2014@users.noreply.github.com> 2020-10-15 15:13:50 -0400;
  • fc801f270 Version bump by sherman5 <tomsherman159@gmail.com> 2020-08-09 21:13:21 -0400;
  • dc5bd3ac5 Merge branch 'master' of git.bioconductor.org:packages/CoGAPS by sherman5 <tomsherman159@gmail.com> 2020-08-09 21:05:30 -0400;
  • f8784a31a Fix some bugs in the documentation by sherman5 <tomsherman159@gmail.com> 2020-06-30 01:53:52 -0400;
  • 8841e6911 Fix bug with death-rebirth by sherman5 <tomsherman159@gmail.com> 2020-06-29 04:34:34 -0400;
  • 3b82dadef 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 18:22:38 +0000;
  • d54e9ec76 (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 18:22:38 +0000;
  • 6bf603a19 Merge pull request <a href="#50">#50</a> from lothm2014/master by lothm2014 <59892258+lothm2014@users.noreply.github.com> 2020-04-23 19:46:16 -0400;
  • 265c3aa53 Removed packageDescription from citation file by lothm2014 <lothm2014@yahoo.com> 2020-04-23 19:33:14 -0400;
  • 3a77a5b8a Merge pull request <a href="#45">#45</a> from FertigLab/develop by archana64 <47166902+archana64@users.noreply.github.com> 2019-11-26 10:22:17 -0500;
  • a50fbb453 Merge branch 'master' into develop by sherman5 <tomsherman159@gmail.com> 2019-11-25 22:17:59 -0500;
  • 7e99466b1 Allow Bioc devel builds to fail on Travis by sherman5 <tomsherman159@gmail.com> 2019-11-25 22:14:10 -0500;
  • 978d0a5e3 Merge pull request <a href="#38">#38</a> from FertigLab/developerArchana by archana64 <47166902+archana64@users.noreply.github.com> 2019-11-12 13:08:28 -0500;
  • 323e0cd72 Added methods getAmplitudeMatrix and getPatternMatrix by Archana Balan <archanabalan@Archanas-MacBook-Pro.local> 2019-11-12 12:10:54 -0500;
  • d1189fcf3 Added methods getAmplitudeMatrix and getPatternMatrix by Archana Balan <archanabalan@Archanas-MacBook-Pro.local> 2019-11-12 12:10:26 -0500;
  • e2f29b980 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 13:35:17 -0400;
  • 97325f775 (origin/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 13:08:16 -0400;
  • acbe14528 Remove the Rhdf5lib paths from the linking step by sherman5 <tomsherman159@gmail.com> 2019-10-15 01:45:58 -0400;
  • e9125888a print warning to indicate singleCell has been depracated by sherman5 <tomsherman159@gmail.com> 2019-10-15 01:23:10 -0400;
  • 4e0cc12ea remove singleCell parameter, always calculate non-zero mean by Tom Sherman <tomsherman159@gmail.com> 2019-10-03 13:18:49 -0400;
  • 7c859a75c Merge branch 'master' into develop by Tom Sherman <tomsherman159@gmail.com> 2019-09-11 16:20:18 -0400;
  • 2c4f12281 shorten iterations for debug runs by Tom Sherman <tomsherman159@gmail.com> 2019-09-09 21:44:44 -0400;
  • 97eec9b0d Merge branch 'master' into develop by Tom Sherman <tomsherman159@gmail.com> 2019-09-09 21:24:37 -0400;
  • 12d9c25a6 version bump 3.5.13 by Tom Sherman <tomsherman159@gmail.com> 2019-09-09 21:24:27 -0400;
  • e942d9ce6 Fixed parameter initialization error by Tom Sherman <tomsherman159@gmail.com> 2019-09-09 20:41:52 -0400;
  • c3b53cb31 Fix up remaining errors during package check by Tom Sherman <tomsherman159@gmail.com> 2019-09-09 19:42:33 -0400;
  • f0aade346 Updated example data with new slots by Tom Sherman <tomsherman159@gmail.com> 2019-09-09 15:45:00 -0400;
  • acf06fdea Updated documentation for new slot names by Tom Sherman <tomsherman159@gmail.com> 2019-09-09 14:57:33 -0400;
  • 652404f54 Change std dev slots in CogapsResult by Tom Sherman <tomsherman159@gmail.com> 2019-09-05 16:59:43 -0400;
  • 5cba79bf4 fix number of iterations used in vignette by Tom Sherman <tomsherman159@gmail.com> 2019-09-05 16:47:09 -0400;
  • ce457ed80 tidied up notation around pattern markers by Tom Sherman <tomsherman159@gmail.com> 2019-09-05 14:14:53 -0400;
  • c4b0894c2 Changed default nIterations to 50K by Tom Sherman <tomsherman159@gmail.com> 2019-09-05 14:14:41 -0400;
  • e914127bd Snapshots working for both phases by Tom Sherman <tomsherman159@gmail.com> 2019-09-04 20:20:30 -0400;
  • 85084e57e Added option to take snapshots during sampling by Tom Sherman <tomsherman159@gmail.com> 2019-09-03 11:23:59 -0400;
  • 542ad9350 Version bump 3.5.12 by Tom Sherman <tomsherman159@gmail.com> 2019-08-30 14:22:36 -0400;
  • a3832b7a0 Updated man page for calcZ by Tom Sherman <tomsherman159@gmail.com> 2019-08-30 14:22:25 -0400;
  • 4d26f1a7b Fixed failing example for calcZ by Tom Sherman <tomsherman159@gmail.com> 2019-08-30 14:20:17 -0400;
  • f6825c25e Version bump 3.5.11 by Tom Sherman <tomsherman159@gmail.com> 2019-08-30 13:42:06 -0400;
  • 198795751 Change zeros in StdDev Matrix to a warning by Tom Sherman <tomsherman159@gmail.com> 2019-08-30 13:40:16 -0400;
  • 376b78ddd Set minimum p-value in permutation test by Tom Sherman <tomsherman159@gmail.com> 2019-08-30 13:38:53 -0400;
  • 8244f8a9d Version bump 3.5.10 by Tom Sherman <tomsherman159@gmail.com> 2019-08-30 13:35:53 -0400;
  • f9bd7d01b Fix bogus error check by Tom Sherman <tomsherman159@gmail.com> 2019-08-30 13:34:26 -0400;
  • a9f6b0c9e Version bump 3.5.9 by sherman5 <tomsherman159@gmail.com> 2019-08-29 19:37:50 -0400;
  • 2443775ad Enable calcCoGAPSStat for P Matrix by sherman5 <tomsherman159@gmail.com> 2019-08-29 19:34:55 -0400;
  • 209e4471f Version bump by Tom Sherman <tomsherman159@gmail.com> 2019-07-22 17:39:52 -0400;
  • 3f7f901d0 Added handler for scientific notation in input by Tom Sherman <tomsherman159@gmail.com> 2019-07-22 17:37:24 -0400;
  • 52d37d1c6 Version bump by Tom Sherman <tomsherman159@gmail.com> 2019-07-22 16:52:45 -0400;
  • 2ac581010 Correct the parsing in mtx files by Tom Sherman <tomsherman159@gmail.com> 2019-07-22 16:46:20 -0400;
  • 2ea9901e2 Remove ccache usage on Travis for Mac by Tom Sherman <tomsherman159@gmail.com> 2019-07-17 17:53:25 -0400;
  • d33100ed0 Use clang for Travis builds on Mac by Tom Sherman <tomsherman159@gmail.com> 2019-07-17 17:38:03 -0400;