Graph of methrix
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• (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_18 branch by 2023-10-24 11:17:51 -0400;
• (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by 2023-10-24 11:17:51 -0400;
• fix BC errors by 2023-09-29 11:14:01 +0200;
• fixing missing dependency error by 2023-09-20 01:06:33 +0200;
• bump x.y.z version to odd y following creation of RELEASE_3_17 branch by 2023-04-25 11:13:54 -0400;
• (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by 2023-04-25 11:13:54 -0400;
• bump x.y.z version to odd y following creation of RELEASE_3_16 branch by 2022-11-01 11:20:54 -0400;
• (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by 2022-11-01 11:20:54 -0400;
• Merge pull request <a href="#29">#29</a> from maurerv/master by 2022-05-27 12:16:30 +0530;
• Update write_bedgraphs.R by 2022-05-21 12:03:41 +0200;
• bump x.y.z version to odd y following creation of RELEASE_3_15 branch by 2022-04-26 16:00:56 +0000;
• (origin/RELEASE_3_15, RELEASE_3_15) bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by 2022-04-26 16:00:56 +0000;
• remove dup loci by 2021-12-02 12:17:51 +0100;
• bump x.y.z version to odd y following creation of RELEASE_3_14 branch by 2021-10-26 16:55:50 +0000;
• (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by 2021-10-26 16:55:50 +0000;
• bump x.y.z version to odd y following creation of RELEASE_3_13 branch by 2021-05-19 16:47:45 +0000;
• (origin/RELEASE_3_13, RELEASE_3_13) bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by 2021-05-19 16:47:45 +0000;
• BC 3.13 RC by 2021-05-12 11:10:41 +0200;
• Thank you @hpages for the fixes on BC devel by 2021-05-04 14:04:37 +0200;
• Please NEVER use direct slot access e.g. don't do 'm@assays\$data\$beta' by 2021-05-01 15:34:18 -0700;
• Update serialized methrix object 'methrix_data' by 2021-05-01 14:49:13 -0700;
• Fix <a href="#26">#26</a> by 2021-03-05 10:48:54 +0100;
• (origin/RELEASE_3_12, RELEASE_3_12) version bump for bioC by 2021-02-11 09:54:37 +0100;
• fix bioC error by 2021-02-11 09:00:54 +0100;
• update issues url by 2021-02-09 15:55:10 +0100;
• remove rjson, update URL by 2021-02-09 15:54:30 +0100;
• version bump by 2021-02-09 09:02:43 +0100;
• update screeplot/report, version bump by 2021-02-08 17:10:44 +0100;
• Merge branch 'master' of https://github.com/CompEpigen/methrix by 2021-02-08 16:20:54 +0100;
• add citation by 2021-02-08 16:20:20 +0100;
• better handle of chromosome names Add MT support to remove_snps() by 2020-12-22 01:45:44 +0100;
• DelayedArray write_block x back to sink by 2020-12-22 01:45:00 +0100;
• bump x.y.z version to odd y following creation of RELEASE_3_12 branch by 2020-10-27 11:51:15 -0400;
• bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by 2020-10-27 11:51:15 -0400;
• Bioc 3.12 RC by 2020-10-23 16:54:21 +0200;
• BioC 3.12 RC by 2020-10-19 12:30:05 +0200;
• update vignette by 2020-10-16 12:23:17 +0200;
• update readme by 2020-10-16 12:19:14 +0200;
• BioC devel fix by 2020-10-15 16:28:30 +0200;
• remove delayedarray version req by 2020-10-14 16:40:54 +0200;
• delayedarray sink to x by 2020-10-13 15:47:03 +0200;
• update BC devel by 2020-10-13 15:41:43 +0200;
• update readme by 2020-10-13 15:35:38 +0200;
• update to fit the new methrix version by 2020-10-12 09:19:46 +0200;
• resync with DelayedArray 0.15.16 by 2020-10-08 22:25:26 -0700;
• typo by 2020-10-07 14:13:45 +0200;
• include prefix into report name by 2020-10-07 14:12:00 +0200;
• added write_bigWigs() by 2020-10-07 11:18:27 +0200;
• Merge branch 'master' of https://github.com/CompEpigen/methrix by 2020-10-01 16:19:50 +0200;
• update write_bedgraphs() to multiBed and metilene by 2020-10-01 16:25:30 +0200;
• update read_bedgraphs to support other callers by 2020-10-01 15:08:38 +0200;
• version by 2020-09-08 10:47:10 +0200;
• push to devel by 2020-09-08 10:42:44 +0200;
• remove travis CI by 2020-09-08 10:13:55 +0200;
• Version bump, devel error fix by 2020-09-08 10:12:11 +0200;
• formatting fixing bug in get_region_summary by 2020-08-14 14:50:59 +0200;
• Merge pull request <a href="#21">#21</a> from CompEpigen/super_big by 2020-07-16 14:19:29 +0200;
• Delete methrix_super_big.Rproj by 2020-07-13 03:43:15 +0200;
• revised tests moved GenomicRanges and IRanges from Suggested packages to imported packages in DESCRIPTION by 2020-07-13 03:38:12 +0200;
• get_region_summary function by 2020-07-08 23:54:47 +0200;
• get_region_summary function Adding NAMESPACE, DESCRIPTION for import functions by 2020-07-05 20:09:30 +0200;
• 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 2020-07-05 19:08:43 +0200;
• 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 2020-07-05 19:08:43 +0200;
• 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 2020-07-05 19:06:19 +0200;
• 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 2020-07-05 19:03:20 +0200;
• remove_uncovered function * changed from data.table to matrixStats. by 2020-07-05 19:02:04 +0200;
• 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 2020-07-03 05:36:10 +0200;
• (origin/RELEASE_3_11, RELEASE_3_11) Fix BioC warnings by 2020-05-30 12:15:39 +0200;
• fix Bioc warnings by 2020-05-29 13:57:09 +0200;
• version bump by 2020-05-03 09:00:32 +0200;
• bump x.y.z version to odd y following creation of RELEASE_3_11 branch by 2020-04-27 19:32:12 +0000;
• bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by 2020-04-27 19:32:12 +0000;
• Merge pull request <a href="#20">#20</a> from ClarissaFeuersteinAkgoz/master by 2020-04-02 08:39:51 +0200;
• Update methrix_plot.R by 2020-04-01 15:14:43 +0200;
• Update write_bedgraphs.Rd by 2020-03-31 15:13:58 +0200;
• Merge pull request <a href="#19">#19</a> from ClarissaFeuersteinAkgoz/master by 2020-03-31 11:15:54 +0200;
• Update write_bedgraphs.R by 2020-03-31 10:21:15 +0200;
• Merge pull request <a href="#2">#2</a> from CompEpigen/master by 2020-03-31 09:48:54 +0200;
• Address <a href="#17">#17</a> by 2020-03-30 13:39:24 +0200;
• (origin/RELEASE_3_10, RELEASE_3_10) merge with master by 2020-01-08 09:35:32 +0100;
• Fix <a href="#12">#12</a> by 2020-01-06 14:19:40 +0100;
• fix parse_source_idx bug by 2019-12-23 12:10:29 +0100;
• namespace update by 2019-12-18 16:07:48 +0100;
• added argument documentation by 2019-12-13 12:39:13 +0100;
• Merge branch 'master' of https://github.com/CompEpigen/methrix by 2019-12-13 11:10:01 +0100;
• change order in get_region_summary bugfix in methrix_plot by 2019-12-12 09:16:00 +0100;
• version bump by 2019-12-02 17:20:45 +0100;
• Merge branch 'master' of https://github.com/CompEpigen/methrix by 2019-12-02 14:25:26 +0100;
• fix sorting order by 2019-12-02 13:54:24 +0100;
• Merge branch 'master' of https://github.com/CompEpigen/methrix by 2019-12-02 13:28:38 +0100;
• fixed return object by 2019-12-02 10:40:06 +0100;
• fix conflict by 2019-12-02 10:09:01 +0100;
• bump version by 2019-12-02 10:07:06 +0100;
• Add keep option to snp removal update documentation by 2019-12-02 09:18:44 +0100;
• Merge branch 'master' of https://github.com/CompEpigen/methrix by 2019-12-02 09:10:30 +0100;
• Merge branch 'master' of https://github.com/CompEpigen/methrix by 2019-11-29 13:06:30 +0100;
• 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 2019-11-29 13:04:41 +0100;
• beta estimation row sampling fix by 2019-11-26 14:27:27 +0100;
• bump x.y.z version to odd y after creation of RELEASE_3_10 branch by 2019-10-29 13:43:47 -0400;