- GSVA
- Graph
-
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;