Graph ofHiCBricks
  • *
  • *
  • *
  • *
  • *
  • *
  • |\
  • * |
  • * |
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • * |
  • |\ \
  • | |/
  • |/|
  • | *
  • * |
  • * |
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • |\
  • * \
  • |\ \
  • * | |
  • | * |
  • |/ /
  • * |
  • * |
  • * |
  • | *
  • | *
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • |\
  • * |
  • * |
  • | *
  • |/|
  • | *
  • | |\
  • | |/
  • |/|
  • * |
  • * |
  • |\|
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • |/
  • *
  • *
  • |\
  • * |
  • * |
  • * |
  • * |
  • * |
  • |\ \
  • * | |
  • | | *
  • | | *
  • | |/
  • |/|
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • |/
  • *
  • *
  • *
  • 4ade93e (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 15:51:41 +0000;
  • 5a6994b (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 15:51:41 +0000;
  • 2a085ec version bump by Koustav <koustavpal1988@gmail.com> 2022-01-01 12:34:42 +0000;
  • c0ebe71 Modified more writedataset functions to reflect change in underlying rhdf5 function names by Koustav <koustavpal1988@gmail.com> 2022-01-01 12:33:04 +0000;
  • fd8d30f version bump by Koustav <koustavpal1988@gmail.com> 2021-12-29 13:55:46 +0000;
  • b0bd68d Merge branch 'master' of git.bioconductor.org:packages/HiCBricks by Koustav <koustavpal1988@gmail.com> 2021-12-29 13:54:24 +0000;
  • 47bed6f version bump by Koustav <koustavpal1988@gmail.com> 2021-12-27 16:31:55 +0000;
  • 6221afa changed h5writedataset function by Koustav <koustavpal1988@gmail.com> 2021-12-27 16:30:45 +0000;
  • 59e90be 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 16:47:36 +0000;
  • 595fc2b (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 16:47:36 +0000;
  • 238cbbd 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 16:38:53 +0000;
  • f242bbd (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 16:38:53 +0000;
  • d2c648e 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 11:39:46 -0400;
  • 12ba995 (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 11:39:46 -0400;
  • 30c15e2 Merge branch 'master' of github.com:koustav-pal/HiCBricks Merging changes made to README by Koustav Pal <koustav.pal@ifom.eu> 2020-05-02 10:15:17 +0200;
  • d6e2b72 Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2020-04-29 10:48:11 +0200;
  • 09ac355 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 19:20:41 +0000;
  • 853214f (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 19:20:41 +0000;
  • be5e9dd - Fixed errors and warnings in sparse loading documentation - version bump by Koustav Pal <koustav.pal@ifom.eu> 2020-03-02 09:50:43 +0100;
  • 70363f3 - changed citation to bibentry - version bump by Koustav Pal <koustav.pal@ifom.eu> 2020-02-28 09:20:16 +0100;
  • 54f0cad - Changed citation - version bump by Koustav Pal <koustav.pal@ifom.eu> 2020-02-27 23:55:27 +0100;
  • d141dcf - Added citation - Fixed documentation error - version bump by Koustav Pal <koustav.pal@ifom.eu> 2020-02-27 23:47:46 +0100;
  • 128acb6 Final push before bioconductor devel check by Koustav Pal <koustav.pal@ifom.eu> 2020-02-25 17:19:19 +0100;
  • 8563703 Added dontrun chunk to the load data from sparse script by Koustav Pal <koustav.pal@ifom.eu> 2020-02-25 15:09:32 +0100;
  • 1e97350 Fixed the sparse loading function - created entries in the vignette for the loading of sparse matrices. by Koustav Pal <koustav.pal@ifom.eu> 2020-02-25 14:21:28 +0100;
  • 75b76aa Added variables to example outputs by Koustav Pal <koustav.pal@ifom.eu> 2020-02-24 21:28:48 +0100;
  • 3fa7472 Merge branch 'master' of git.bioconductor.org:packages/HiCBricks by Koustav Pal <koustav.pal@ifom.eu> 2020-02-24 20:56:02 +0100;
  • 06ca557 Merge branch 'master' of github.com:koustav-pal/HiCBricks by Koustav Pal <koustav.pal@ifom.eu> 2020-02-24 20:52:28 +0100;
  • 3b7b2f7 - Fixed table loading function. - Added support for sparse matrices. - Created the sparse loading function Brick_load_data_from_sparse by Koustav Pal <koustav.pal@ifom.eu> 2020-02-24 20:49:36 +0100;
  • 5a098df Changed the Brick_get_chrominfo function such that now the json file is used to create the chrominfo. This commit is part of a larger set of commits - to implement parallelization - to remove dependency on HDF attributes by Koustav Pal <koustavpal@Koustavs-MacBook-Pro.local> 2020-02-17 15:21:47 +0100;
  • 74ebe05 Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-11-29 14:03:26 +0100;
  • 2d112b5 Updated README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-11-22 10:24:09 +0100;
  • a2f597c Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-11-01 08:29:16 +0100;
  • 6296425 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 13:43:21 -0400;
  • cf9b736 (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 13:11:24 -0400;
  • a77ea34 Minor change to the vignette by Koustav Pal <koustavpal1988@gmail.com> 2019-09-26 00:16:17 +0200;
  • c72f7dc Modified vignette text by Koustav Pal <koustavpal1988@gmail.com> 2019-09-26 00:10:41 +0200;
  • 48dcb5f Changed the DESCRIPTION file by Koustav Pal <koustav.pal@ifom.eu> 2019-09-25 16:14:59 +0200;
  • b084cc6 Version bump by Koustav Pal <koustav.pal@ifom.eu> 2019-09-13 15:13:18 +0200;
  • dfcaa26 made compartment calling faster by Koustav Pal <koustav.pal@ifom.eu> 2019-09-13 15:12:30 +0200;
  • 677a1a9 - Added function to call compartments. - Fixed the colour bar so that the ticks are now properly represented. - Added a function to fetch entire matrices by Koustav Pal <koustav.pal@ifom.eu> 2019-09-13 14:31:26 +0200;
  • a99c94e Bugfix to vignette by Koustav Pal <koustav.pal@ifom.eu> 2019-09-07 16:24:20 +0200;
  • 34c8a57 Small change to the vignette by Koustav Pal <koustav.pal@ifom.eu> 2019-09-07 16:06:35 +0200;
  • 01647e1 Added method to convert BrickContainer to mcool files by Koustav Pal <koustav.pal@ifom.eu> 2019-09-07 16:05:10 +0200;
  • 1559305 Fixed cooler loader such that both lower and upper triangles are loaded when the write buffer is near the main diagonal by Koustav Pal <koustav.pal@ifom.eu> 2019-09-02 17:50:49 +0200;
  • 65c8407 bugfix for export to sparse by Koustav Pal <koustav.pal@ifom.eu> 2019-09-02 11:51:35 +0200;
  • 528b5b1 Bugfix for viz_art function TAD lines computation by Koustav Pal <koustav.pal@ifom.eu> 2019-09-02 11:50:19 +0200;
  • aa29c47 Fixed vapply bug in LSD by Koustav Pal <koustav.pal@ifom.eu> 2019-09-02 11:08:53 +0200;
  • 8ebacda - Bugfix to plotting function. - Fixed the bug wherein two TADs called under two different colour groups were not being considered separately. - Bugfix to LSD - If chrs is NULL, then all chromosomes are processed. In such a scenario, if a chromosome pair is not done, this will cause the entire function to fail. Now, chromosomes which are not done are removed. by Koustav Pal <koustav.pal@ifom.eu> 2019-09-02 10:33:49 +0200;
  • 478f53a Pushing bugfixes. by Koustav Pal <koustav.pal@ifom.eu> 2019-08-30 15:50:43 +0200;
  • ccf310e Pushing bugfixes to the cooler loader functions. by Koustav Pal <koustav.pal@ifom.eu> 2019-08-30 13:52:49 +0200;
  • 99a0011 Removed old cooler functions. Implemented new cooler functions. by Koustav Pal <koustav.pal@ifom.eu> 2019-08-29 15:40:40 +0200;
  • 86da8b5 Merge branch 'master' of github.com:koustav-pal/HiCBricks by Koustav Pal <koustav.pal@ifom.eu> 2019-08-29 15:38:39 +0200;
  • 547a05b Implemented changes to cooler loading. It is much simpler now by Koustav Pal <koustav.pal@ifom.eu> 2019-08-29 15:37:06 +0200;
  • 47faf03 bugfixes to vignette by Koustav Pal <koustav.pal@ifom.eu> 2019-08-26 09:39:23 +0200;
  • ee47299 Merge pull request <a href="#11">#11</a> from koustav-pal/development by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-08-25 11:40:58 +0200;
  • 872dfcc Merge pull request <a href="#10">#10</a> from koustav-pal/master by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-08-25 11:40:12 +0200;
  • 517e857 version bump by Koustav Pal <koustav.pal@ifom.eu> 2019-08-24 14:35:26 +0200;
  • a8d50f6 Merge pull request <a href="#9">#9</a> from koustav-pal/development by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-08-24 12:42:52 +0200;
  • 5a59f63 Another bugfix for Brick_export_to_sparse by Koustav Pal <koustav.pal@ifom.eu> 2019-08-24 12:19:30 +0200;
  • 690fa34 Bugfix for Brick_export_to_sparse by Koustav Pal <koustav.pal@ifom.eu> 2019-08-24 12:18:00 +0200;
  • 6937d09 - removed dplyr::arrange dependency and replaced it with order by Koustav Pal <koustav.pal@ifom.eu> 2019-08-24 11:56:34 +0200;
  • 18288a7 Final finishing touches to the package before major devel branch closure by Koustav Pal <koustav.pal@ifom.eu> 2019-08-24 10:52:56 +0200;
  • 974f403 bug fixes by Koustav Pal <koustavpal1988@gmail.com> 2019-08-24 00:41:53 +0200;
  • ae24231 changed row.sum parameter name in vignette to chr1_row_sums by Koustav Pal <koustavpal1988@gmail.com> 2019-08-23 21:33:56 +0200;
  • c605bdd Added Brick_export_to_sparse by Koustav Pal <koustav.pal@ifom.eu> 2019-08-23 18:43:53 +0200;
  • 7bee732 table loading complete without a metrics by Koustav Pal <koustavpal1988@gmail.com> 2019-08-21 18:26:24 +0200;
  • 7921320 Intermediate work on the table loader functions by Koustav Pal <koustav.pal@ifom.eu> 2019-08-20 17:06:53 +0200;
  • 378a0b7 Rewriting the table loading function by Koustav Pal <koustavpal1988@gmail.com> 2019-08-20 10:40:04 +0200;
  • c7f71a6 removed cooler_loaders file. unlink_resolution now issues a message instead of a warning by Koustav Pal <koustavpal1988@gmail.com> 2019-08-19 21:09:33 +0200;
  • a128113 creatd basic table loading function by Koustav Pal <koustav.pal@ifom.eu> 2019-08-19 20:22:13 +0200;
  • e813fdc Removed the usage of the exec parameter by Koustav Pal <koustavpal1988@gmail.com> 2019-08-19 00:28:36 +0200;
  • fb79dd2 Bugfixes and finally all examples have passed and vignette building is complete by Koustav Pal <koustav.pal@ifom.eu> 2019-08-14 17:43:07 +0200;
  • af47efd Bug fixes for BrickContainer functions by Koustav Pal <koustav.pal@ifom.eu> 2019-08-13 20:48:21 +0200;
  • 6a22d57 Made major changes to the Brick workflow. Now bricks are stored as separate files. Functions for parallelization has been added. This is an unstable build. by Koustav Pal <koustav.pal@ifom.eu> 2019-08-09 17:18:42 +0200;
  • 468635a version bump by Koustav Pal <koustav.pal@ifom.eu> 2019-05-24 14:00:45 +0200;
  • 3aa0776 Merge remote-tracking branch 'upstream/master' by Koustav Pal <koustav.pal@ifom.eu> 2019-05-24 13:53:29 +0200;
  • 86397db Version bump by Koustav Pal <koustav.pal@ifom.eu> 2019-05-24 12:02:56 +0200;
  • ef85df0 More bugfixes to cooler import by Koustav Pal <koustav.pal@ifom.eu> 2019-05-24 12:02:16 +0200;
  • 93a9b05 Changed the vignette header information by Koustav Pal <koustav.pal@ifom.eu> 2019-05-24 10:57:57 +0200;
  • f8daea2 Changed travis to release branch by Koustav Pal <koustav.pal@ifom.eu> 2019-05-24 10:40:12 +0200;
  • bfe681c Merge branch 'master' of github.com:koustav-pal/HiCBricks by Koustav Pal <koustav.pal@ifom.eu> 2019-05-23 18:05:18 +0200;
  • af8fef2 Bugfixes - Fixed a bug in cool import, where only one chromosome structure was being created. - Fixed a discrepancy between how format-version is found in mcool files. - Fixed a bug where if the binsize was left NULL it would cause and error during mcool import. by Koustav Pal <koustav.pal@ifom.eu> 2019-05-23 18:02:32 +0200;
  • 99195e1 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 12:15:57 -0400;
  • e2a588c (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 11:54:13 -0400;
  • 09e12cd Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-29 10:38:58 +0100;
  • 0aa6b88 Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-29 10:38:28 +0100;
  • 38db794 Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-29 10:37:59 +0100;
  • dc7951d Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-29 10:35:50 +0100;
  • 8a1bb3f Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-29 10:35:31 +0100;
  • 1bc00d0 Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-29 10:34:57 +0100;
  • 9c4387b Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-29 10:34:26 +0100;
  • 6bed0dd Update README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-28 14:36:14 +0100;
  • a3f558a Added Bioconductor logo to README by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-28 14:35:54 +0100;
  • a0213a0 Update .RbuildIgnore to ignore README by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-28 13:42:58 +0100;
  • 90efba6 Created README.md by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-28 13:42:05 +0100;
  • c7c0411 Adding codecov support to travis by Koustav Pal <koustav-pal@users.noreply.github.com> 2019-03-27 21:53:20 +0100;
  • 4d7426e Pushing bugfixes to Brick_add_ranges example by Koustav Pal <koustav.pal@ifom.eu> 2019-03-27 18:36:19 +0100;
  • ab00a61 Fixed bugs in examples and deleted references to biocfilecache in manpages by Koustav Pal <koustav.pal@ifom.eu> 2019-03-27 16:07:43 +0100;
  • 93763bf Pushing a small change to trigger travis ci by Koustav Pal <koustav.pal@ifom.eu> 2019-03-27 15:27:21 +0100;