53cd9ea (HEAD -> devel, origin/master, origin/devel, origin/HEAD) 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 11:29:55 -0400;
33bf569 (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 11:29:55 -0400;
a4eede2 Merge branch 'devel' by
Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au>2023-03-21 12:41:42 +1030;
dcc6b2d Fix typo. by
Ahmed Mohamed <amfy10@gmail.com>2023-03-21 02:44:52 +1100;
b7ccc57 Fixed the edge case where networks of all groups are empty by
Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au>2023-03-20 16:04:18 +1030;
15bce61 Fix GHA failures. by
Ahmed Mohamed <amfy10@gmail.com>2023-01-03 12:15:10 +1100;
da819cf Upgate GHA verisons. by
Ahmed Mohamed <amfy10@gmail.com>2022-12-20 14:12:47 +1100;
d7d76b8 Enable setting `org` for PPI networks. by
Ahmed Mohamed <amfy10@gmail.com>2022-12-20 14:05:51 +1100;
4ff3a5f 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 11:25:00 -0400;
6ebddf9 (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 11:25:00 -0400;
2d00f72 Update GHA envir versions by
bhuva.d <bhuva.d@wehi.edu.au>2022-10-13 11:21:57 +1100;
76d357e replaced stopifnot checks with new checking functions to produce interpretable errors by
bhuva.d <bhuva.d@wehi.edu.au>2022-10-12 21:38:47 +1100;
0efa76a updated check functions by
bhuva.d <bhuva.d@wehi.edu.au>2022-10-12 21:36:08 +1100;
c395f0b change param names by
bhuva.d <bhuva.d@wehi.edu.au>2022-10-12 15:49:00 +1100;
e20e387 added error reporting functions by
bhuva.d <bhuva.d@wehi.edu.au>2022-10-12 15:34:43 +1100;
e30a8bc Update parameters for network plot by
bhuva.d <bhuva.d@wehi.edu.au>2022-10-11 10:46:38 +1100;
4b2a67d 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 16:16:02 +0000;
f897fcb (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 16:16:02 +0000;
b3007a3 Add codecov badge by
bhuva.d <bhuva.d@wehi.edu.au>2022-03-17 13:03:02 +1100;
7fb73ad Add logo to readme by
bhuva.d <bhuva.d@wehi.edu.au>2022-03-17 12:57:07 +1100;
8d4d907 Remove KEGG download from vignette to simplify checks on Windows machines. by
bhuva.d <bhuva.d@wehi.edu.au>2022-03-17 12:01:58 +1100;
7c2436e Bugfix in fingMsigClusters by
bhuva.d <bhuva.d@wehi.edu.au>2022-02-28 11:16:52 +1100;
f935d96 Fixed bug in plotMsigPPI function by
bhuva.d <bhuva.d@wehi.edu.au>2022-02-12 14:03:49 +1100;
474c829 Added new terms to the blacklist. by
bhuva.d <bhuva.d@wehi.edu.au>2022-02-08 10:34:58 +1100;
fa96412 Bug fix: explicit call to median function by
bhuva.d <bhuva.d@wehi.edu.au>2021-12-08 12:31:26 +1100;
b7c0d22 Added missing documentation by
bhuva.d <bhuva.d@wehi.edu.au>2021-12-08 11:26:10 +1100;
e11c023 Added function to identify and prioritise gene-set clusters. by
bhuva.d <bhuva.d@wehi.edu.au>2021-12-08 09:06:26 +1100;
53d590a Update workflow params by
bhuva.d <bhuva.d@wehi.edu.au>2021-12-07 12:00:03 +1100;
061ec10 Added the Adjusted Rand Index (ARI) as a measure of gene-set overlap. by
bhuva.d <bhuva.d@wehi.edu.au>2021-12-07 11:29:53 +1100;
d256c9d Bug fix in plotPPI by
bhuva.d <bhuva.d@wehi.edu.au>2021-12-04 11:52:27 +1100;
ea9c63c Fixed statName bug in plotMsigPPI by
bhuva.d <bhuva.d@wehi.edu.au>2021-12-03 11:18:21 +1100;
5f40401 the gene-set overlap network can now be filtered to display only those categories selected in groups. by
bhuva.d <bhuva.d@wehi.edu.au>2021-12-03 11:02:33 +1100;
a17f141 Added rank to PPI and fixed bugs by
bhuva.d <bhuva.d@wehi.edu.au>2021-11-05 11:56:31 +1100;
ae414a7 Revert pkgdown workflow to use deploy_to_branch by
Ahmed Mohamed <amfy10@gmail.com>2021-10-29 12:15:26 +1100;
690dee2 (origin/RELEASE_3_14, RELEASE_3_14) Fixed broken example by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-28 13:24:53 +1100;
cfa3b93 Fixed broken example by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-28 13:23:25 +1100;
e43d375 Fixed broken example by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-28 13:21:30 +1100;
c2bd9e6 Fixed test cases by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-28 11:48:09 +1100;
d9a382a Fixed test cases by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-28 11:46:50 +1100;
de6b3b8 Fix test cases. by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-28 11:40:34 +1100;
64645e1 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 17:09:59 +0000;
ad4cf81 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 17:09:59 +0000;
0443e51 Update default Jaccard threshold (0.25 mostly works better) by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-23 12:54:25 +1100;
1443ff1 Changed default word cloud statistic by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-20 12:04:17 +1100;
f5b93de Added missing documentation value and removed unrequired dependencies by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-13 07:27:37 +1100;
824dd92 Update blacklist for msigdb v7.3 onwards by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-12 17:16:21 +1100;
d43cebf Merge pull request <a href="#7">#7</a> from DavisLaboratory/feature-docs-improvements by
Dharmesh Bhuva <bhuva.d@wehi.edu.au>2021-10-12 16:54:57 +1100;
18066f8 Added PPI plot example in the vignettes by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-12 16:10:50 +1100;
ff88fcc Bug fixes in checks for edge cases by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-12 16:10:13 +1100;
ce0f1e8 Bug fixes and added test cases for PPI plotting function. by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-12 11:56:00 +1100;
c772c40 Explicitly pass PPI as input. by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-12 11:08:00 +1100;
6b87656 Check gene-set groups using a dedicated function by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-12 11:07:27 +1100;
ad3adfa bug fix with network plotting function by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-12 08:37:35 +1100;
19e81c6 Bug fix on PPI network - uses inferred PPI information by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-11 21:09:26 +1100;
f895f72 Added functionality to explore PPIs for each gene-set cluster by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-11 20:54:28 +1100;
a68cbb7 Bug fix: fixed issue with wordcloud plots by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-11 18:17:34 +1100;
bd3718d Specify organism type for characterise gene-set function by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-11 17:53:39 +1100;
7e5b1c0 Allow manual selection of organism in wordcloud computation by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-11 17:26:12 +1100;
62de88b Updated plotting funtion to label genes based on rank rather than binary variable by
bhuva.d <bhuva.d@wehi.edu.au>2021-10-11 11:41:30 +1100;
4b0b1e5 update pkgdown action; remove unnecessary gitignore by
Ahmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>2021-09-29 11:42:37 +1000;
1c267db Update README; add badges by
Ahmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>2021-09-29 11:35:39 +1000;
ac16e46 Bug fix plotMaigWordcloud by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-23 15:58:14 +1000;
348c6d3 Added additional checks for edge cases by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-23 14:30:01 +1000;
b1dea86 Remove characteriseGeneset function from vignette by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-19 18:58:45 +1000;
5dfa0fc Fix github actions and update plot combination code. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-19 17:19:48 +1000;
9c00334 Add allow_failure attribute for all jobs by
Ahmed Mohamed <amfy10@gmail.com>2021-08-19 12:21:45 +1000;
d393f2c Merge branch 'main' of github.com:DavisLaboratory/vissE into main by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-19 12:11:35 +1000;
4c4636c Added pkgdown yaml by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-19 12:09:11 +1000;
053617e allow CI failures on windows by
Ahmed Mohamed <amfy10@gmail.com>2021-08-19 11:55:53 +1000;
8441b07 Disable window's check until curl has been built by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-19 11:52:35 +1000;
ab0fb25 Install windows curl dependency by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-19 11:19:20 +1000;
2d76b94 Add Rtools to path for github actions by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-19 11:11:59 +1000;
e8b256a Delete old data objects and their scripts. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-18 22:12:01 +1000;
6191e97 Correct bugs in the vignette and in characteriseGeneset by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-18 20:58:45 +1000;
ef2f40b Added bioc github actions by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-18 17:15:15 +1000;
ce91009 Bug fix in mark groups and updated news file. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-12 15:53:18 +1000;
c990ff4 Update line width parameter in plot. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-12 15:19:42 +1000;
9822053 Ported network plotting to ggraph. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-12 15:14:21 +1000;
3380bcd Removed unnecessary text-mining warnings and added version param to specify the version of MSigDB to use for IDF values. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-12 13:25:48 +1000;
266b644 Remove precomputation of the incidence matrix (upto 10000 gene-sets can run in ~10s). by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-11 23:38:57 +1000;
59aef2a updated word cloud weighting computation and test cases. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-09 21:37:14 +1000;
7d80f4b Remove normalisation step for weights used in the word cloud. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-09 21:21:23 +1000;
a0db8b8 Update weighting strategy by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-09 20:58:42 +1000;
9a6c885 Added weighting for word cloud computation. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-09 20:32:02 +1000;
fcf56ed Update documentation for ploting function. by
bhuva.d <bhuva.d@wehi.edu.au>2021-08-09 19:24:22 +1000;
ca86ba2 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 17:03:31 +0000;
1a90b74 (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 17:03:31 +0000;
dabc1d8 Bug fix for using external data as internal data within the package. by
Dharmesh Bhuva <bhuva.d@wehi.edu.au>2021-05-10 17:27:15 +1000;
92ad722 Reference data directly since lazy loading has been disabled. by
Dharmesh Bhuva <bhuva.d@wehi.edu.au>2021-05-10 16:30:10 +1000;
ee63700 Used seq_len() following suggestions from notes. by
Dharmesh Bhuva <bhuva.d@wehi.edu.au>2021-05-10 16:28:32 +1000;
3707d8c Removed lazy data by
Dharmesh Bhuva <bhuva.d@wehi.edu.au>2021-05-10 12:08:46 +1000;
d8bb9ce Removed evaluation of installation code from vignettes. by
Dharmesh Bhuva <bhuva.d@wehi.edu.au>2021-05-10 12:08:15 +1000;
cafb455 Created documentation for the package. by
Dharmesh Bhuva <bhuva.d@wehi.edu.au>2021-05-10 11:33:15 +1000;
330e2f5 Removed one news file by
Dharmesh Bhuva <bhuva.d@wehi.edu.au>2021-05-10 11:32:28 +1000;
df1aa06 Version bump to trigger SPB build by
bhuva.d <bhuva.d@wehi.edu.au>2021-04-27 09:46:44 +1000;
5dd0be8 Lazy compression by
bhuva.d <bhuva.d@wehi.edu.au>2021-04-26 08:40:32 +1000;
1b97894 Reduced package file size by reducing the number of pre-computed results. by
bhuva.d <bhuva.d@wehi.edu.au>2021-04-23 22:16:21 +1000;
221d884 Updated test cases for IDF computation by
bhuva.d <bhuva.d@wehi.edu.au>2021-04-23 22:15:46 +1000;
ef98199 Bug fix for indexing in intersection computation functions. by
bhuva.d <bhuva.d@wehi.edu.au>2021-04-23 22:02:04 +1000;
