Bioconductor Code: scAnnotatR

Graph of scAnnotatR

a0da05e (HEAD -> devel, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_21 branch by A Wokaty <[email protected]> 2025-04-15 12:37:49 -0400;
b025898 (origin/RELEASE_3_21, RELEASE_3_21) bump x.y.z version to even y prior to creation of RELEASE_3_21 branch by A Wokaty <[email protected]> 2025-04-15 12:37:49 -0400;
108d23b (origin/master) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by J Wokaty <[email protected]> 2024-10-29 11:03:50 -0400;
a89857e (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by J Wokaty <[email protected]> 2024-10-29 11:03:50 -0400;
77000fc bump x.y.z version to odd y following creation of RELEASE_3_19 branch by J Wokaty <[email protected]> 2024-04-30 11:36:58 -0400;
cc77d19 (origin/RELEASE_3_19, RELEASE_3_19) bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by J Wokaty <[email protected]> 2024-04-30 11:36:58 -0400;
7763087 Fixed bug in classify_cells_sce by Johannes Griss <[email protected]> 2024-04-01 21:01:29 +0200;
92d3ee6 Fix vignettes by Johannes Griss <[email protected]> 2024-03-21 15:09:36 +0100;
a93358f bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <[email protected]> 2023-10-24 11:36:04 -0400;
5367b84 (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 <[email protected]> 2023-10-24 11:36:04 -0400;
be90c8a bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <[email protected]> 2023-04-25 11:32:25 -0400;
b567a90 (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 <[email protected]> 2023-04-25 11:32:25 -0400;
0850995 Fixed <a href="#9">#9</a> Commit to Bioconductor by Johannes Griss <[email protected]> 2023-03-19 19:49:15 +0100;
a4bd9e0 Addresses <a href="#9">#9</a> Added "ambiguous_chars" parameter by Johannes Griss <[email protected]> 2023-03-17 23:02:16 +0100;
3b93845 Merge branch 'develop' by Johannes Griss <[email protected]> 2023-03-05 22:29:31 +0100;
f4e12ee Fixes <a href="#7">#7</a> Automatically add required parent classifiers by Johannes Griss <[email protected]> 2023-03-05 22:28:07 +0100;
6c8cd89 Addresses <a href="#7">#7</a> Adapted error message by Johannes Griss <[email protected]> 2023-02-23 20:32:15 +0100;
09fd0fb Adapted version number and news by Johannes Griss <[email protected]> 2023-01-17 21:41:06 +0100;
7fed668 Merge remote-tracking branch 'bioc/master' by Johannes Griss <[email protected]> 2023-01-17 21:38:05 +0100;
11cd44b Fix issue about marker genes by nttvy <[email protected]> 2023-01-18 01:00:10 +0700;
dd19ebf bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <[email protected]> 2022-11-01 11:25:35 -0400;
90e7357 (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 <[email protected]> 2022-11-01 11:25:35 -0400;
f7ff91d bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <[email protected]> 2022-04-26 16:18:05 +0000;
e9d43a6 (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 <[email protected]> 2022-04-26 16:18:05 +0000;
0e57e79 fix bug in subsetting classifiers in classifying Seurat objects by nttvy <[email protected]> 2022-03-28 16:35:24 +0200;
88442ac Update paper citation by nttvy <[email protected]> 2022-01-23 12:34:06 +0100;
f219b1a bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <[email protected]> 2021-10-26 17:12:15 +0000;
c896512 (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 <[email protected]> 2021-10-26 17:12:15 +0000;
9db2ee8 merge master and develop branch by nttvy <[email protected]> 2021-09-15 23:25:28 +0200;
1bd749c adapt model download function to use AnnotationHub by nttvy <[email protected]> 2021-09-15 23:17:08 +0200;
42af6a6 remove BiocFileCache use by nttvy <[email protected]> 2021-08-17 13:17:47 +0200;
19b46a0 Adapted examples to improve runtime by Johannes Griss <[email protected]> 2021-08-03 21:09:02 +0200;
6ed07e6 Version bump to test auto build by Johannes Griss <[email protected]> 2021-08-03 16:34:22 +0200;
a2d8fb1 (origin/develop, develop) Moved to version 0.99.4 by Johannes Griss <[email protected]> 2021-07-30 16:20:36 +0200;
9d571f2 Disable use of BiocFileCache::bfcneedsupdate by Johannes Griss <[email protected]> 2021-07-30 15:54:09 +0200;
35ed297 Fixed typo by Johannes Griss <[email protected]> 2021-07-30 15:53:47 +0200;
1f9ce47 solve issue caused by gene symbols starting by digits by nttvy <[email protected]> 2021-07-30 04:41:57 +0200;
7114049 merge separate classify cells methods for SCE and Seurat obj into one function by nttvy <[email protected]> 2021-07-30 03:15:08 +0200;
506e25a add preprocess function for SCE and Seurat obj used in training and testing process by nttvy <[email protected]> 2021-07-30 01:24:40 +0200;
a212ecf merge separate methods for Seurat and SCE signatures into one function by nttvy <[email protected]> 2021-07-30 00:23:02 +0200;
a5d06e3 remove default_models store in package, use BiocFileCache to manage pretrained models by nttvy <[email protected]> 2021-07-29 16:57:11 +0200;
92331be fix bug by _p by nttvy <[email protected]> 2021-07-29 01:45:01 +0200;
b867bca reduce duplication code in train_classifier and test_classifier remove parameter signature in support functions by nttvy <[email protected]> 2021-07-29 01:43:14 +0200;
1253f44 Version bump to trigger new BioConductor build. by Johannes Griss <[email protected]> 2021-07-24 19:49:12 +0200;
8891045 add NEWS file by nttvy <[email protected]> 2021-07-23 20:14:54 +0200;
05a39d6 bump package version by nttvy <[email protected]> 2021-07-22 21:36:59 +0200;
adb6f19 replace core clf by caret_model replace all other clf by classifiers by nttvy <[email protected]> 2021-07-22 15:51:48 +0200;
7e9ee09 change features to marker_genes by nttvy <[email protected]> 2021-07-22 13:32:05 +0200;
97b79e7 change default file path to tempdir avoid using / in file paths, use file.path instead by nttvy <[email protected]> 2021-07-21 15:52:16 +0200;
44b4dc6 use empty environment to load data by nttvy <[email protected]> 2021-07-21 14:26:12 +0200;
a599c91 use setReplaceMethod instead of creating normal functional setters for object components by nttvy <[email protected]> 2021-07-20 23:46:58 +0200;
f92ca6b export models in vignettes to tempdir instead of current directory by nttvy <[email protected]> 2021-07-20 13:35:28 +0200;
f376790 fix DESCRIPTION file based on reviews by nttvy <[email protected]> 2021-07-20 13:12:09 +0200;
099328c convert scClassifR objects to scAnnotatR objects by nttvy <[email protected]> 2021-07-20 11:37:09 +0200;
f5a3043 reduce clfs file size by nttvy <[email protected]> 2021-07-01 22:50:50 +0200;
fb25249 change to version 0.99.1 by nttvy <[email protected]> 2021-07-01 20:25:56 +0200;
31595bc change version to 0.99 for new submission by nttvy <[email protected]> 2021-07-01 19:16:03 +0200;
0c5f4fe update default_models infomation by nttvy <[email protected]> 2021-07-01 14:31:42 +0200;
dd14a53 remove Rproj file by nttvy <[email protected]> 2021-07-01 14:25:35 +0200;
9e893a8 adapt README file to new package name by nttvy <[email protected]> 2021-07-01 14:24:05 +0200;
499496a rename package from scClassifR to scAnnotatR by nttvy <[email protected]> 2021-07-01 14:02:51 +0200;
8b3d175 change R v4.1 dependency by nttvy <[email protected]> 2021-06-30 00:17:48 +0200;
c7e26bf fix bug when using certain clfs by calling clfs name by nttvy <[email protected]> 2021-06-19 12:16:40 +0200;
7ed74c1 remove commented code by nttvy <[email protected]> 2021-06-19 03:39:08 +0200;
71f93b3 optimize prediction simplification process by nttvy <[email protected]> 2021-06-19 01:27:04 +0200;
12a40c6 fix bug in announcing ambiguous cells fix bug in checking positive child cells when tag slot is stored in active.ident by nttvy <[email protected]> 2021-06-04 14:26:20 +0200;
49e8d5e Fix bug because of underscore in cell type by nttvy <[email protected]> 2021-06-01 14:23:20 +0200;
0ded936 update all new clfs by nttvy <[email protected]> 2021-06-01 13:17:00 +0200;
546a63b fix error when only one clf used for classification and subsets containing no corresponding predicted cell type by nttvy <[email protected]> 2021-05-31 19:43:49 +0200;
3350b9c fix show method by nttvy <[email protected]> 2021-05-31 00:58:47 +0200;
c66b6fb fix bug in selecting features for child clfs by nttvy <[email protected]> 2021-05-30 22:35:45 +0200;
b78b63b add warning when ambiguous cell types are found by nttvy <[email protected]> 2021-05-30 20:17:41 +0200;
f21f5c0 fix ambiguous pattern related to 'or' by nttvy <[email protected]> 2021-05-30 19:54:37 +0200;
3a36898 fix bug to preserve matrix dimension when only one feature is selected by nttvy <[email protected]> 2021-05-30 19:47:51 +0200;
bf6e949 fix bug to keep the right dimension by nttvy <[email protected]> 2021-05-30 00:39:30 +0200;
b2dda0f fix warning in cluster prediction by nttvy <[email protected]> 2021-05-09 22:48:51 +0200;
28d2daa update default clfs using new training kernel by nttvy <[email protected]> 2021-04-20 18:14:07 +0200;
7dfeff6 fix bug in cluster prediction: duplication in cluster prediction generates error by nttvy <[email protected]> 2021-04-20 00:15:47 +0200;
b1933cc add param for predicted chunk size by nttvy <[email protected]> 2021-04-15 20:50:22 +0200;
0e2f5b0 remove printing head of trained matrix by nttvy <[email protected]> 2021-04-14 00:21:54 +0200;
a2773db change scaling strategy in train and test function: scale gene expression before filter out parent cell types by nttvy <[email protected]> 2021-04-13 23:34:58 +0200;
e76953c fix bug in z-score calculation when split classified data into chunks by nttvy <[email protected]> 2021-04-12 00:20:51 +0200;
cd61993 divide data into chunks when classifying cells to reduce running time by nttvy <[email protected]> 2021-04-11 01:34:30 +0200;
6c63e3c add cluster prediction by nttvy <[email protected]> 2021-04-10 19:44:04 +0200;
be07e5e solve issue caused by hypen (-) in feature symbols by nttvy <[email protected]> 2021-03-24 20:58:03 +0100;
0d4a895 change kernel training function by nttvy <[email protected]> 2021-03-22 22:34:16 +0100;
b74288e Addresses #5. Reverted R version requirement by Johannes Griss <[email protected]> 2021-03-10 11:40:18 +0100;
5ac5f9e Moved to 0.99.6 to trigger build by Johannes Griss <[email protected]> 2021-01-11 20:34:54 +0100;
3f85b6e Updated README with new package name by Johannes Griss <[email protected]> 2020-12-29 20:09:10 +0100;
89852fb Merge pull request <a href="#3">#3</a> from grisslab/develop by Johannes Griss <[email protected]> 2020-12-29 20:07:10 +0100;
0ed9c39 rename package by nttvy <[email protected]> 2020-12-29 01:49:20 +0100;
73dff4d add eval = FALSe to the code chunks involving package installation by nttvy <[email protected]> 2020-12-24 23:29:17 +0100;
a09741e change vector comparison to improve readability by nttvy <[email protected]> 2020-12-24 23:15:00 +0100;
378dd1f use message() when reporting progress by nttvy <[email protected]> 2020-12-24 22:01:20 +0100;
324a82f improve nested expressions by nttvy <[email protected]> 2020-12-24 21:26:27 +0100;
c8374b1 change indentation style to improve readability by nttvy <[email protected]> 2020-12-24 20:58:42 +0100;
b7e67a7 Merge branch 'develop' of https://github.com/grisslab/scTypeR into develop by nttvy <[email protected]> 2020-12-24 17:12:28 +0100;
6c81450 convert single-method generics to plain-old functions by nttvy <[email protected]> 2020-12-24 17:11:58 +0100;
7ebd31e Re-added NEWS file with proper content. by Johannes Griss <[email protected]> 2020-12-23 20:50:28 +0100;
7e29eda use accessors instead of @ by nttvy <[email protected]> 2020-12-22 23:05:24 +0100;