1. methrix
  2. Graph
Graph of methrix
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  • 8a77091 (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 11:17:51 -0400;
  • 6ed5233 (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 11:17:51 -0400;
  • 62f7a75 fix BC errors by Anand <anandmt3@gmail.com> 2023-09-29 11:14:01 +0200;
  • fa4fb8c fixing missing dependency error by tkik <rtoth81@gmail.com> 2023-09-20 01:06:33 +0200;
  • e118d02 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 11:13:54 -0400;
  • 7e3f893 (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 11:13:54 -0400;
  • 1131980 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 11:20:54 -0400;
  • c93ba71 (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 11:20:54 -0400;
  • 21f9732 Merge pull request <a href="#29">#29</a> from maurerv/master by Anand Mayakonda <anandmt3@gmail.com> 2022-05-27 12:16:30 +0530;
  • c7006c8 Update write_bedgraphs.R by Valentin Maurer <43959863+maurerv@users.noreply.github.com> 2022-05-21 12:03:41 +0200;
  • ebec736 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 16:00:56 +0000;
  • 321ca92 (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 16:00:56 +0000;
  • 46b375f remove dup loci by PoisonAlien <anandmt3@gmail.com> 2021-12-02 12:17:51 +0100;
  • 0475e22 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 16:55:50 +0000;
  • 19065b7 (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 16:55:50 +0000;
  • 6e33fe4 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 16:47:45 +0000;
  • 74b8250 (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 16:47:45 +0000;
  • 4e04643 BC 3.13 RC by PoisonAlien <anandmt3@gmail.com> 2021-05-12 11:10:41 +0200;
  • 219929f Thank you @hpages for the fixes on BC devel by PoisonAlien <anandmt3@gmail.com> 2021-05-04 14:04:37 +0200;
  • 93d4504 Please NEVER use direct slot access e.g. don't do 'm@assays$data$beta' by Hervé Pagès <hpages.on.github@gmail.com> 2021-05-01 15:34:18 -0700;
  • 4170082 Update serialized methrix object 'methrix_data' by Hervé Pagès <hpages.on.github@gmail.com> 2021-05-01 14:49:13 -0700;
  • b6be3f3 Fix <a href="#26">#26</a> by PoisonAlien <anandmt3@gmail.com> 2021-03-05 10:48:54 +0100;
  • 012a4cc (origin/RELEASE_3_12, RELEASE_3_12) version bump for bioC by PoisonAlien <anandmt3@gmail.com> 2021-02-11 09:54:37 +0100;
  • 2ffc504 fix bioC error by PoisonAlien <anandmt3@gmail.com> 2021-02-11 09:00:54 +0100;
  • ef6ea59 update issues url by PoisonAlien <anandmt3@gmail.com> 2021-02-09 15:55:10 +0100;
  • 66d5168 remove rjson, update URL by PoisonAlien <anandmt3@gmail.com> 2021-02-09 15:54:30 +0100;
  • b622315 version bump by PoisonAlien <anandmt3@gmail.com> 2021-02-09 09:02:43 +0100;
  • 3f01422 update screeplot/report, version bump by PoisonAlien <anandmt3@gmail.com> 2021-02-08 17:10:44 +0100;
  • 22d6d54 Merge branch 'master' of https://github.com/CompEpigen/methrix by PoisonAlien <anandmt3@gmail.com> 2021-02-08 16:20:54 +0100;
  • 4f4b4c3 add citation by PoisonAlien <anandmt3@gmail.com> 2021-02-08 16:20:20 +0100;
  • 6cd7fcf better handle of chromosome names Add MT support to remove_snps() by tkike <rtoth81@gmail.com> 2020-12-22 01:45:44 +0100;
  • 14eb43c DelayedArray write_block x back to sink by tkike <rtoth81@gmail.com> 2020-12-22 01:45:00 +0100;
  • 7c1dac3 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 11:51:15 -0400;
  • 82d505c 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 11:51:15 -0400;
  • 5d5087c Bioc 3.12 RC by PoisonAlien <anandmt3@gmail.com> 2020-10-23 16:54:21 +0200;
  • 7192eda BioC 3.12 RC by PoisonAlien <anandmt3@gmail.com> 2020-10-19 12:30:05 +0200;
  • f8bf890 update vignette by PoisonAlien <anandmt3@gmail.com> 2020-10-16 12:23:17 +0200;
  • d3b3721 update readme by PoisonAlien <anandmt3@gmail.com> 2020-10-16 12:19:14 +0200;
  • a6f65e7 BioC devel fix by mayakond <mayakond@canepi-srv1.inet.dkfz-heidelberg.de> 2020-10-15 16:28:30 +0200;
  • a767059 remove delayedarray version req by Anand Mayakonda <anandmt3@gmail.com> 2020-10-14 16:40:54 +0200;
  • 518d9b9 delayedarray sink to x by PoisonAlien <anandmt3@gmail.com> 2020-10-13 15:47:03 +0200;
  • f0a1011 update BC devel by PoisonAlien <anandmt3@gmail.com> 2020-10-13 15:41:43 +0200;
  • 093f6c6 update readme by PoisonAlien <anandmt3@gmail.com> 2020-10-13 15:35:38 +0200;
  • 4740679 update to fit the new methrix version by tkike <rtoth81@gmail.com> 2020-10-12 09:19:46 +0200;
  • 3551897 resync with DelayedArray 0.15.16 by Hervé Pagès <hpages.on.github@gmail.com> 2020-10-08 22:25:26 -0700;
  • 2cdaa88 typo by tkike <rtoth81@gmail.com> 2020-10-07 14:13:45 +0200;
  • ce67d1a include prefix into report name by tkike <rtoth81@gmail.com> 2020-10-07 14:12:00 +0200;
  • 477be9e added write_bigWigs() by PoisonAlien <anandmt3@gmail.com> 2020-10-07 11:18:27 +0200;
  • e57220e Merge branch 'master' of https://github.com/CompEpigen/methrix by PoisonAlien <anandmt3@gmail.com> 2020-10-01 16:19:50 +0200;
  • f9648ba update write_bedgraphs() to multiBed and metilene by poisonalien <anandmt3@gmail.com> 2020-10-01 16:25:30 +0200;
  • 6802b52 update read_bedgraphs to support other callers by poisonalien <anandmt3@gmail.com> 2020-10-01 15:08:38 +0200;
  • 8db7c0b version by PoisonAlien <anandmt3@gmail.com> 2020-09-08 10:47:10 +0200;
  • 8090a13 push to devel by PoisonAlien <anandmt3@gmail.com> 2020-09-08 10:42:44 +0200;
  • 42b0aa1 remove travis CI by PoisonAlien <anandmt3@gmail.com> 2020-09-08 10:13:55 +0200;
  • 047efd7 Version bump, devel error fix by PoisonAlien <anandmt3@gmail.com> 2020-09-08 10:12:11 +0200;
  • 3b6d61e formatting fixing bug in get_region_summary by tkike <rtoth81@gmail.com> 2020-08-14 14:50:59 +0200;
  • 56583d7 Merge pull request <a href="#21">#21</a> from CompEpigen/super_big by Anand Mayakonda <anandmt3@gmail.com> 2020-07-16 14:19:29 +0200;
  • 1d52ad4 Delete methrix_super_big.Rproj by rnbatra <Rajbir.batra@dkfz.de> 2020-07-13 03:43:15 +0200;
  • 556ad7d revised tests moved GenomicRanges and IRanges from Suggested packages to imported packages in DESCRIPTION by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-13 03:38:12 +0200;
  • 7da4b19 get_region_summary function by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-08 23:54:47 +0200;
  • b0c8de4 get_region_summary function Adding NAMESPACE, DESCRIPTION for import functions by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-05 20:09:30 +0200;
  • 608151f get_region_summary function * need to check where to add libraries. * added parameter ‘elementMetadata.col’ to enable summarisation of specific columns in elementMetadata. * add column ‘rid’ to mention what row of methrix object. * fixed order of rows (looks like this has already been fixed recently on master). * fixed order of columns to keep chr, start, end at the beginning. * added n_chunks (memory) and n_cores (parallel) support both HDF5 and in-memory methrix objects. by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-05 19:08:43 +0200;
  • 2abaa28 get_region_summary function * need to check where to add libraries. * added parameter ‘elementMetadata.col’ to enable summarisation of specific columns in elementMetadata. * add column ‘rid’ to mention what row of methrix object. * fixed order of rows (looks like this has already been fixed recently on master). * fixed order of columns to keep chr, start, end at the beginning. * added n_chunks (memory) and n_cores (parallel) support both HDF5 and in-memory methrix objects. by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-05 19:08:43 +0200;
  • b999ad2 coverage_filter function * changed to matrix stats. * corrected order of output rows to reflect input order. * added parameter prop_samples - % of samples which is especially useful when using group as a stratifier. * Quicker processing. * added n_chunks (memory) and n_cores (parallel) support both HDF5 and in-memory methrix objects. by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-05 19:06:19 +0200;
  • 7d55e46 remove_snps function * removed maf threshold restriction. * fixed error 'could not find function 'populations'. * added n_chunks (memory) and n_cores (parallel) support for HDF5 methrix objects. * added time taken message. by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-05 19:03:20 +0200;
  • 6d2cdbf remove_uncovered function * changed from data.table to matrixStats. by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-05 19:02:04 +0200;
  • 033ba18 mask_methrix function * added details of number of CpG sites masked due to low coverage (so now gives similar information as removed due to high coverage). * added n_chunks (memory) and n_cores (parallel) support only for HDF5 methrix objects. by Rajbir N Batra <rajbir.batra@dkfz.de> 2020-07-03 05:36:10 +0200;
  • ccc4e39 (origin/RELEASE_3_11, RELEASE_3_11) Fix BioC warnings by PoisonAlien <anandmt3@gmail.com> 2020-05-30 12:15:39 +0200;
  • 719a4f8 fix Bioc warnings by Mayakonda Thippeswamy <mayakond@vm-130-12.cloud.dkfz-heidelberg.de> 2020-05-29 13:57:09 +0200;
  • 1846246 version bump by PoisonAlien <anandmt3@gmail.com> 2020-05-03 09:00:32 +0200;
  • f626072 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 19:32:12 +0000;
  • e4bcbaf 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 19:32:12 +0000;
  • d2e3860 Merge pull request <a href="#20">#20</a> from ClarissaFeuersteinAkgoz/master by Anand Mayakonda <anandmt3@gmail.com> 2020-04-02 08:39:51 +0200;
  • 24c70e7 Update methrix_plot.R by ClarissaFeuersteinAkgoz <48914703+ClarissaFeuersteinAkgoz@users.noreply.github.com> 2020-04-01 15:14:43 +0200;
  • e5d87ea Update write_bedgraphs.Rd by ClarissaFeuersteinAkgoz <48914703+ClarissaFeuersteinAkgoz@users.noreply.github.com> 2020-03-31 15:13:58 +0200;
  • 503bbf1 Merge pull request <a href="#19">#19</a> from ClarissaFeuersteinAkgoz/master by Anand Mayakonda <anandmt3@gmail.com> 2020-03-31 11:15:54 +0200;
  • 68714f1 Update write_bedgraphs.R by ClarissaFeuersteinAkgoz <48914703+ClarissaFeuersteinAkgoz@users.noreply.github.com> 2020-03-31 10:21:15 +0200;
  • 7ee5ad4 Merge pull request <a href="#2">#2</a> from CompEpigen/master by ClarissaFeuersteinAkgoz <48914703+ClarissaFeuersteinAkgoz@users.noreply.github.com> 2020-03-31 09:48:54 +0200;
  • 61e7907 add comment by PoisonAlien <anandmt3@gmail.com> 2020-03-30 13:42:33 +0200;
  • 4f84991 Address <a href="#17">#17</a> by PoisonAlien <anandmt3@gmail.com> 2020-03-30 13:39:24 +0200;
  • 2ae3aae (origin/RELEASE_3_10, RELEASE_3_10) merge with master by PoisonAlien <anandmt3@gmail.com> 2020-01-08 09:35:32 +0100;
  • 43066e8 Fix <a href="#12">#12</a> by poisonalien <anandmt3@gmail.com> 2020-01-06 14:19:40 +0100;
  • 59405c5 fix parse_source_idx bug by poisonalien <anandmt3@gmail.com> 2019-12-23 12:10:29 +0100;
  • 0ef7e26 namespace update by Toth <tothr@ad.dkfz-heidelberg.de> 2019-12-18 16:07:48 +0100;
  • 67f2e46 added argument documentation by Toth <tothr@ad.dkfz-heidelberg.de> 2019-12-13 12:39:13 +0100;
  • 9820546 Merge branch 'master' of https://github.com/CompEpigen/methrix by Toth <tothr@ad.dkfz-heidelberg.de> 2019-12-13 11:10:01 +0100;
  • 8571a3b change order in get_region_summary bugfix in methrix_plot by Toth <tothr@ad.dkfz-heidelberg.de> 2019-12-12 09:16:00 +0100;
  • ff56192 version bump by poisonalien <anandmt3@gmail.com> 2019-12-02 17:20:45 +0100;
  • 48ceb0e Merge branch 'master' of https://github.com/CompEpigen/methrix by poisonalien <anandmt3@gmail.com> 2019-12-02 14:25:26 +0100;
  • 392cef3 fix sorting order by Toth <tothr@ad.dkfz-heidelberg.de> 2019-12-02 13:54:24 +0100;
  • 04dcc64 Merge branch 'master' of https://github.com/CompEpigen/methrix by poisonalien <anandmt3@gmail.com> 2019-12-02 13:28:38 +0100;
  • b708b35 fixed return object by Toth <tothr@ad.dkfz-heidelberg.de> 2019-12-02 10:40:06 +0100;
  • d0112dc fix conflict by poisonalien <anandmt3@gmail.com> 2019-12-02 10:09:01 +0100;
  • 31e9cbb bump version by poisonalien <anandmt3@gmail.com> 2019-12-02 10:07:06 +0100;
  • 6bfde48 Add keep option to snp removal update documentation by Toth <tothr@ad.dkfz-heidelberg.de> 2019-12-02 09:18:44 +0100;
  • 9cee100 Merge branch 'master' of https://github.com/CompEpigen/methrix by poisonalien <anandmt3@gmail.com> 2019-12-02 09:10:30 +0100;
  • 3ed1fab Merge branch 'master' of https://github.com/CompEpigen/methrix by Toth <tothr@ad.dkfz-heidelberg.de> 2019-11-29 13:06:30 +0100;
  • 6446ea8 Bugfixes in coverage_filter Bugfixes in subset_methrix Group argument in coverage_filter Prefix argument in methrix_report keep option in snp_removal minor fixes in plotting functions by Toth <tothr@ad.dkfz-heidelberg.de> 2019-11-29 13:04:41 +0100;
  • 97823df beta estimation row sampling fix by poisonalien <anandmt3@gmail.com> 2019-11-26 14:27:27 +0100;
  • 57777a3 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 13:43:47 -0400;