Bioconductor Code: GSVA

Graph of GSVA

cc23576 (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 09:46:46 -0400;
72a1f51 (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 09:46:46 -0400;
53effda Updated NEWS file by Robert Castelo <robert.castelo@upf.edu> 2023-10-20 18:48:28 +0200;
cca01b5 Merge pull request <a href="#120">#120</a> from rcastelo/new_api by Robert Castelo <robert.castelo@upf.edu> 2023-10-20 18:11:38 +0200;
9769607 Merge pull request <a href="#119">#119</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-10-20 16:30:14 +0200;
954fbd6 update unit tests for parameter objects and new API by Axel Klenk <axel.klenk@gmail.com> 2023-10-20 16:20:51 +0200;
dd22a0a unify handling and add checking of new arguments 'annotation' and 'assay'. move some utility functions to R/utils.R (!) by Axel Klenk <axel.klenk@gmail.com> 2023-10-19 22:51:13 +0200;
4d9ecd5 Merge pull request <a href="#118">#118</a> from rcastelo/new_api by Robert Castelo <robert.castelo@upf.edu> 2023-10-11 16:49:30 +0200;
c71f1b2 Merge pull request <a href="#117">#117</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-10-09 17:24:13 +0200;
87a2e83 add show() methods for parameter objects that re-use components' show where appropriate and override them otherwise by Axel Klenk <axel.klenk@gmail.com> 2023-10-09 17:07:45 +0200;
25165ca Merge pull request <a href="#111">#111</a> from rcastelo/new_api by Robert Castelo <robert.castelo@upf.edu> 2023-09-25 20:45:49 +0200;
424dc39 Improving consistency in the documentation of help pages and vignette in the new API by Robert Castelo <robert.castelo@upf.edu> 2023-09-25 19:55:21 +0200;
c7f48ad Merge pull request <a href="#110">#110</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-25 17:16:16 +0200;
30a33bd migrate vignette to new API; work around eSet/annotation() problem by Axel Klenk <axel.klenk@gmail.com> 2023-09-25 16:43:55 +0200;
8994ac4 Merge pull request <a href="#109">#109</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-25 13:29:06 +0200;
82c2696 add slots and constructor arguments for 'annotation', 'minSize', and 'maxSize' to parameter objects; remove the latter two from gsva() by Axel Klenk <axel.klenk@gmail.com> 2023-09-25 13:21:06 +0200;
ba3a6f8 Merge pull request <a href="#108">#108</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-24 22:16:22 +0200;
a18b04b Add argument 'assay' to parameter objects to make example(gsva) work. by Axel Klenk <axel.klenk@gmail.com> 2023-09-24 22:01:04 +0200;
b0d132a Fixed documentation and other stuff by Robert Castelo <robert.castelo@upf.edu> 2023-09-21 17:47:45 +0200;
36f7ebe Merge pull request <a href="#107">#107</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-21 14:01:29 +0200;
aa61b1e add code and docs for deprecation of old interface; add docs for new interface; eliminate argument parallel.sz; fix .gitignore by Axel Klenk <axel.klenk@gmail.com> 2023-09-21 13:57:22 +0200;
7ca884b Merge pull request <a href="#106">#106</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-15 23:49:26 +0200;
7e94844 no idea what git is doing to me here... by Axel Klenk <axel.klenk@gmail.com> 2023-09-15 23:28:03 +0200;
0bb99f0 fix .gitignore to have man/*.Rd files properly tracked. by Axel Klenk <axel.klenk@gmail.com> 2023-09-15 23:13:55 +0200;
d123bc4 fix .gitignore to have man/*.Rd files properly tracked. by Axel Klenk <axel.klenk@gmail.com> 2023-09-15 23:13:55 +0200;
31d7e7f Merge pull request <a href="#105">#105</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-15 19:57:40 +0200;
efd45fc Merge branch 'dev_new_api' into new_api by Axel Klenk <axel.klenk@gmail.com> 2023-09-15 19:49:29 +0200;
6f94311 New API first version, more documentation and unit tests to be added; existing code using the 'old' API should continue work. by Axel Klenk <axel.klenk@gmail.com> 2023-09-15 19:41:39 +0200;
87d6258 Merge pull request <a href="#104">#104</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-13 16:40:50 +0200;
3db1522 Merge branch 'dev_new_api' into new_api by Axel Klenk <axel.klenk@gmail.com> 2023-09-13 15:40:19 +0200;
fb72959 add show methods for parameter classes. by Axel Klenk <axel.klenk@gmail.com> 2023-09-13 15:38:31 +0200;
e478814 restore previous gsva generic and method signatures by Axel Klenk <axel.klenk@gmail.com> 2023-09-13 13:20:46 +0200;
0bdf1c0 Merge pull request <a href="#103">#103</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-12 17:09:01 +0200;
25e70ea Merge branch 'dev_new_api' into new_api by Axel Klenk <axel.klenk@gmail.com> 2023-09-12 16:52:15 +0200;
0a2f8df Initial implementation of New API for all methods and gene set containers and almost all data containers. (TODO: continue refactoring, document and test.) by Axel Klenk <axel.klenk@gmail.com> 2023-09-12 14:53:02 +0200;
da4e6b1 add class unions for new_api next step by Axel Klenk <axel.klenk@gmail.com> 2023-09-06 11:29:27 +0200;
f92d4c6 Merge branch 'dev_new_api' into new_api by Axel Klenk <axel.klenk@gmail.com> 2023-09-05 10:02:42 +0200;
8b3c590 add regression test based on the vignette and an output file for comparison generated by the released version by Axel Klenk <axel.klenk@gmail.com> 2023-09-04 14:19:51 +0200;
dfeab61 add an experimental regression test based on the vignette -- work in progress! by Axel Klenk <axel.klenk@gmail.com> 2023-09-04 09:16:03 +0200;
cd9abfb add rnorm() and rpois() to NAMESPACE imports and save 'stats::' when using them to generate test data by Axel Klenk <axel.klenk@gmail.com> 2023-09-01 17:47:32 +0200;
cce4456 Merge pull request <a href="#102">#102</a> from axelklenk/new_api by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-09-01 17:08:17 +0200;
27f4b17 add unit tests for dispatch on unnamed arguments. by Axel Klenk <axel.klenk@gmail.com> 2023-09-01 15:58:26 +0200;
743a96f two minor modifications to make the remaining WARNING and NOTE disappear. by Axel Klenk <axel.klenk@gmail.com> 2023-08-31 18:08:34 +0200;
21ac45d document new gsva methods to get rid of check warnings. by Axel Klenk <axel.klenk@gmail.com> 2023-08-30 18:01:28 +0200;
480d69f add unit tests for dispatch by param objects; rename param objects to comply to upper camel case convention. by Axel Klenk <axel.klenk@gmail.com> 2023-08-28 17:21:12 +0200;
0c5e0b4 add matrix/list methods for zscore, ssgsea, gsva; modify to use param for internal dispatch and parameters. Testgit add R/gsvaNewAPI.R by Axel Klenk <axel.klenk@gmail.com> 2023-08-25 18:17:19 +0200;
21fd00e add 'param' argument (as missing) to all 'gsva' S4 methods to silence warnings during check. add roxygen2 documentation for newAPI methods. by Axel Klenk <axel.klenk@gmail.com> 2023-08-25 16:39:15 +0200;
969f0f8 add S4 method for dispatching on PLAGE parameter object by Axel Klenk <axel.klenk@gmail.com> 2023-08-23 17:53:37 +0200;
e444aab add automated generation of test input data by Axel Klenk <axel.klenk@gmail.com> 2023-08-18 19:00:54 +0200;
a08f049 add simple unit tests for method-specific parameter objects and their constructors by Axel Klenk <axel.klenk@gmail.com> 2023-08-14 16:49:59 +0200;
c460cb1 fix --as-cran NOTE on using title case in the package title :-) by Axel Klenk <axel.klenk@gmail.com> 2023-08-01 19:26:58 +0200;
d5b2d25 merge in a couple of unrelated fixes from devel by Axel Klenk <axel.klenk@gmail.com> 2023-08-01 17:03:08 +0200;
0870c68 Merging PR https://github.com/rcastelo/GSVA/pull/99 that improves the parallelization of the zscore method by Robert Castelo <robert.castelo@upf.edu> 2023-07-28 19:30:29 +0200;
9971417 Merge branch 'Liripo-devel' into devel by Robert Castelo <robert.castelo@upf.edu> 2023-07-28 19:28:24 +0200;
db0d616 Merge branch 'devel' of https://github.com/Liripo/GSVA into Liripo-devel by Robert Castelo <robert.castelo@upf.edu> 2023-07-28 18:09:50 +0200;
8314d36 (origin/RELEASE_3_17, RELEASE_3_17) Fixing Codecov badge by Robert Castelo <robert.castelo@upf.edu> 2023-07-27 19:27:10 +0200;
22a955f Bump version by Robert Castelo <robert.castelo@upf.edu> 2023-07-27 19:19:23 +0200;
cd055a8 Fixing Codecov badge by Robert Castelo <robert.castelo@upf.edu> 2023-07-27 19:27:10 +0200;
6a83db1 Fixed bug on C method registration and a couple of --as-cran notes by Robert Castelo <robert.castelo@upf.edu> 2023-07-27 19:19:23 +0200;
5902109 modify zscore by liripo <liripo@qq.com> 2023-07-27 09:07:01 +0800;
2f71756 fix bug in gsvaParam contructor (add match.arg for kcdf, duh); sync slots and parameters documentation for gsvaParam class and constructor by Axel Klenk <axel.klenk@gmail.com> 2023-07-26 14:28:07 +0000;
981dc7b Merge pull request <a href="#98">#98</a> from rcastelo/96-gsva-method-parameter-class-and-constructor by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-07-24 15:32:17 +0200;
a4b627a fix oversight in gsvaParam definition causing a Check error by Axel Klenk <axel.klenk@gmail.com> 2023-07-24 13:29:47 +0000;
093c218 Merge pull request <a href="#97">#97</a> from rcastelo/96-gsva-method-parameter-class-and-constructor by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-07-24 14:46:12 +0200;
e90ee35 Merge branch '96-gsva-method-parameter-class-and-constructor' of github.com:rcastelo/GSVA into 96-gsva-method-parameter-class-and-constructor by Axel Klenk <axel.klenk@gmail.com> 2023-07-24 14:09:26 +0200;
65e233f add gsvaParam class and constructor with argument names and documentation as before; switch from camel case to underscore names for getters (ssgseaParam and gsvaParam); and don't forget to update NAMESPACE by Axel Klenk <axel.klenk@gmail.com> 2023-07-24 11:49:13 +0000;
194b3a8 add gsvaParam class and constructor with argument names and documentation as before; switch from camel case to underscore names for getters (ssgseaParam and gsvaParam) by Axel Klenk <axel.klenk@gmail.com> 2023-07-24 11:49:13 +0000;
e222698 Merge pull request <a href="#95">#95</a> from rcastelo/85-ssgsea-method-parameter-class-and-constructor by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-07-14 17:16:32 +0200;
59a1ea8 ... and don't forget various updates to .gitignore by Axel Klenk <axel.klenk@gmail.com> 2023-07-14 15:00:24 +0000;
dc54f19 finalize ssGSEA; remove allGenerics.R and, on second thoughts, make ssgseaParam getters *functions* instead of methods by Axel Klenk <axel.klenk@gmail.com> 2023-07-14 14:59:31 +0000;
f1008e1 Merge pull request <a href="#94">#94</a> from rcastelo/devel by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-07-10 13:17:17 +0200;
083aaa4 Version bump by Robert Castelo <robert.castelo@upf.edu> 2023-06-23 18:47:38 +0200;
3d3e068 Bugfix in the call to C code by the GSVA algorithm to enable working with long vectors. by Robert Castelo <robert.castelo@upf.edu> 2023-06-23 18:47:38 +0200;
9957f63 Bugfix to correctly deal with a GeneSetCollection object as input gene sets, when the input expression data is a SingleCellExperiment object by Robert Castelo <robert.castelo@upf.edu> 2023-06-01 11:38:07 +0200;
6cceb58 Bugfix to correctly deal with a GeneSetCollection object as input gene sets, when the input expression data is a SingleCellExperiment object by Robert Castelo <robert.castelo@upf.edu> 2023-06-01 11:38:07 +0200;
3874d4c move constructors from allClasses.R to method-specific R files; add class definition, constructor and two get methods for ssGSEA to fix #85; add generics for get methods to new file allGenerics.R by Axel Klenk <axel.klenk@gmail.com> 2023-04-25 14:22:28 +0000;
7fc10d3 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 10:19:44 -0400;
8819055 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 10:19:44 -0400;
c121192 Merge pull request <a href="#84">#84</a> from rcastelo/78-plage-method-parameter-class-and-constructor by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-04-18 14:47:47 +0200;
d1796a1 add PLAGE method parameter class and constructor; modify CITATION to work with both latin1 and UTF-8 encodings by Axel Klenk <axel.klenk@gmail.com> 2023-04-18 12:27:13 +0000;
6aafa42 Merge pull request <a href="#83">#83</a> from rcastelo/73-zscore-method-parameter-class-and-constructor by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-04-17 16:06:06 +0200;
bb2f161 Delete register_cmethods.o by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-04-17 16:02:39 +0200;
ce5c72d Delete ks_test.o by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-04-17 16:02:26 +0200;
4d8e009 Delete kernel_estimation.o by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-04-17 16:02:15 +0200;
9fa3bb0 Delete GSVA.so by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-04-17 16:01:47 +0200;
3a6b337 Merge pull request <a href="#82">#82</a> from rcastelo/devel by Axel Klenk <72612834+axelklenk@users.noreply.github.com> 2023-04-17 15:56:58 +0200;
311e8d3 Updated URL in inst/CITATION file to fix an --as-cran NOTE by Robert Castelo <robert.castelo@upf.edu> 2023-04-17 10:20:49 +0200;
dd6ce2f Bump version by Robert Castelo <robert.castelo@upf.edu> 2023-04-17 10:18:41 +0200;
11d29b0 Merge branch '76-fixing-as-cran-notes-on-the-r-code' into devel by Robert Castelo <robert.castelo@upf.edu> 2023-04-17 10:17:58 +0200;
53738d0 Bump version by Robert Castelo <robert.castelo@upf.edu> 2023-04-17 10:05:51 +0200;
b82b51d fix <a href="#77">#77</a> by adding the missing function call by Axel Klenk <axel.klenk@gmail.com> 2023-04-14 14:35:17 +0000;
9506cd8 fix issue <a href="#76">#76</a> by replacing comparisons of class() with calling inherits() by Axel Klenk <axel.klenk@gmail.com> 2023-04-14 12:11:57 +0000;
8cbada7 fix issue #73: add zscore method parameter class and constructor (and a virtual superclass) by Axel Klenk <axel.klenk@gmail.com> 2023-04-03 17:30:44 +0200;
fd07d5f 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 11:05:54 -0400;
4036d9f (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 11:05:54 -0400;
4ea6b00 Updated NEWS file by Robert Castelo <robert.castelo@upf.edu> 2022-10-31 16:48:30 +0100;
bd55a3a (origin/RELEASE_3_15, RELEASE_3_15) Switching official maintainer to Robert Castelo by Robert Castelo <robert.castelo@upf.edu> 2022-09-20 11:24:51 -0700;
028b188 Switching official maintainer to Robert Castelo by Robert Castelo <robert.castelo@upf.edu> 2022-09-20 11:15:24 -0700;
0c403a9 Enforcing minimum version of the upstream dependency Matrix 1.5-0 by Robert Castelo <robert.castelo@upf.edu> 2022-09-19 23:03:08 -0700;
ac26f36 Enforcing minimum version of the upstream dependency Matrix 1.5-0 by Robert Castelo <robert.castelo@upf.edu> 2022-09-19 22:19:18 -0700;