15bdd09 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) Avoid problems if 'col_data' and 'colData(data)' are identical by
const-ae <artjom31415@googlemail.com>2023-05-05 11:30:51 +0200;
54a6667 (origin/RELEASE_3_17, RELEASE_3_17) Bump version to trigger rebuild and propagation of new Mac binary by
J Wokaty <jwokaty@users.noreply.github.com>2023-05-01 20:10:29 -0400;
9505f48 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 11:16:59 -0400;
5fdfa5c 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 11:16:59 -0400;
937310f Bump version and update NEWS by
const-ae <artjom31415@googlemail.com>2023-03-22 15:23:35 +0100;
5bc7126 Propagate 'ignore_degeneracy' attribute of design to 'test_de' by
const-ae <artjom31415@googlemail.com>2023-03-22 15:23:23 +0100;
78c5cff Add unit test to check if I can handle counts larger than 2^31 by
const-ae <artjom31415@googlemail.com>2023-03-08 16:19:14 +0100;
5573484 Fix bug in error message of `handle_design_parameter` if data was not a matrix by
const-ae <artjom31415@googlemail.com>2023-03-07 19:09:53 +0100;
f2f838e Update NEWS and bump version by
const-ae <artjom31415@googlemail.com>2023-02-27 19:11:27 +0100;
f54f3cd Fix typo in documentation of `overdispersion_shrinkage` function by
const-ae <artjom31415@googlemail.com>2023-02-07 17:08:44 +0100;
052b518 Fix <a href="#44">#44</a> Typo in documentation of 'overdispersion_shrinkage' by
const-ae <artjom31415@googlemail.com>2023-01-31 17:40:19 +0100;
ddfb9f6 Bump version by
const-ae <artjom31415@googlemail.com>2023-01-31 16:39:07 +0100;
7633d5f Improve pseudobulk vignette by
const-ae <artjom31415@googlemail.com>2023-01-31 16:38:35 +0100;
efcb989 (origin/RELEASE_3_16, RELEASE_3_16) Bump version to trigger rebuild and propagation of new Mac binary by
J Wokaty <jwokaty@users.noreply.github.com>2023-01-19 11:17:12 -0500;
aeee8d0 Add tests for 'get_aggregation_function' by
const-ae <artjom31415@googlemail.com>2023-01-18 10:06:07 +0100;
466ed64 Print information in 'pseudobulk' by
const-ae <artjom31415@googlemail.com>2023-01-18 10:05:25 +0100;
3e0b0c0 Make handling of 'offset' matrix safer and add test by
const-ae <artjom31415@googlemail.com>2023-01-13 14:53:10 +0100;
ef91a32 Bump version and update NEWS by
const-ae <artjom31415@googlemail.com>2023-01-13 12:48:23 +0100;
2235c6e Add 'use_assay' argument to 'glm_gp' by
const-ae <artjom31415@googlemail.com>2023-01-13 12:47:42 +0100;
f32d8db Make lines in examples <100 characters to fit within pdf by
const-ae <artjom31415@googlemail.com>2023-01-04 09:59:19 +0100;
a22a6ce Update NEWS and bump version by
const-ae <artjom31415@googlemail.com>2023-01-03 19:08:16 +0100;
77ffa5f Write new vignette on pseudobulk workflow by
const-ae <artjom31415@googlemail.com>2023-01-03 19:08:01 +0100;
ff7b7ac Use new 'pseudobulk' workflow in README by
const-ae <artjom31415@googlemail.com>2023-01-03 19:07:42 +0100;
8f66c3a Check if contrast vector is all zero by
const-ae <artjom31415@googlemail.com>2023-01-03 18:55:02 +0100;
cdfec8e Fix warning from R CMD CHECK by
const-ae <artjom31415@googlemail.com>2023-01-03 17:47:47 +0100;
5f3ed7f Bump roxygen note by
const-ae <artjom31415@googlemail.com>2023-01-03 16:42:43 +0100;
262e3c6 Update documentation of 'test_de' by
const-ae <artjom31415@googlemail.com>2023-01-03 16:41:11 +0100;
a035e3a Deprecate the 'pseudobulk_by' argument in 'test_de' by
const-ae <artjom31415@googlemail.com>2023-01-03 16:41:01 +0100;
4fb8346 Add 'max_lfc' parameter to finally fix problem with gigantic log fold changes in test_de by
const-ae <artjom31415@googlemail.com>2023-01-03 16:40:24 +0100;
62cbe0a Change 'pseudobulk_sce' to 'pseudobulk' by
const-ae <artjom31415@googlemail.com>2023-01-03 16:39:30 +0100;
abe6872 Use rlang quosures for the contrast argument in 'test_de' by
const-ae <artjom31415@googlemail.com>2023-01-03 16:36:04 +0100;
739429d Bump version to trigger rebuild and propagation of new arm64 binary by
J Wokaty <jwokaty@users.noreply.github.com>2022-12-13 18:09:01 -0500;
705787a 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 11:21:46 -0400;
048e173 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 11:21:46 -0400;
0054e54 Fix bug in pseudobulk_sce by
const-ae <artjom31415@googlemail.com>2022-10-24 17:24:25 +0200;
2b5d543 Add example to 'pseudobulk_sce' function by
const-ae <artjom31415@googlemail.com>2022-10-24 17:24:13 +0200;
903e13e Fix warning about missing Matrix import by
const-ae <artjom31415@googlemail.com>2022-10-24 17:22:38 +0200;
3695566 Test some advanced features of 'pseudobulk_sce()' by
const-ae <artjom31415@googlemail.com>2022-10-24 16:23:47 +0200;
58c0114 Change interface of pseudobulk_sce to use 'rlang' idioms by
const-ae <artjom31415@googlemail.com>2022-10-24 15:58:53 +0200;
0d2f778 Aggregate reducedDims in 'pseudobulk_sce' by
const-ae <artjom31415@googlemail.com>2022-09-30 15:28:13 +0200;
11617f3 Add MatrixGenerics to import by
const-ae <artjom31415@googlemail.com>2022-09-30 15:27:37 +0200;
578f917 Bump version and update NEWS by
const-ae <artjom31415@googlemail.com>2022-09-30 15:07:04 +0200;
7839224 Implement 'pseudobulk_sce' to easily form pseudo-bulk samples by
const-ae <artjom31415@googlemail.com>2022-09-30 15:05:51 +0200;
2f78248 Minor code clean-up by
const-ae <artjom31415@googlemail.com>2022-09-30 15:04:40 +0200;
e205bca Bump version and update NEWS by
const-ae <artjom31415@googlemail.com>2022-09-30 15:03:50 +0200;
51e8c55 Refactor eval_with_q by
const-ae <artjom31415@googlemail.com>2022-09-30 15:01:32 +0200;
e7359da 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 16:04:08 +0000;
b723d61 (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 16:04:08 +0000;
054fb65 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 16:58:38 +0000;
03df1e1 (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 16:58:38 +0000;
b595fd7 Bump version by
const-ae <artjom31415@googlemail.com>2021-08-27 11:05:27 +0200;
81e7811 Fix error because SummarizedExperiment now requires matching assay and coldata names by
const-ae <artjom31415@googlemail.com>2021-08-27 11:05:07 +0200;
a04483c Update NEWS and bump version by
const-ae <artjom31415@googlemail.com>2021-08-06 10:42:39 +0200;
494771f Provide better error message if the design matrix contains NA's by
const-ae <artjom31415@googlemail.com>2021-08-06 10:41:11 +0200;
f5d783d Skip mocking tests if not local by
const-ae <artjom31415@googlemail.com>2021-07-01 17:13:26 +0200;
a89a725 Remove R devel from R-CMD-check because Bioconductor cannot handle R4.2 yet by
const-ae <artjom31415@googlemail.com>2021-07-01 14:35:35 +0200;
ba03a11 Bump R version in R-CMD-check workflow by
const-ae <artjom31415@googlemail.com>2021-07-01 14:25:35 +0200;
9bfd4e9 Don't use MulticoreParam in tests on Windows by
const-ae <artjom31415@googlemail.com>2021-07-01 13:53:43 +0200;
763a4b0 Update documentation by
const-ae <artjom31415@googlemail.com>2021-07-01 13:50:23 +0200;
70ba4e7 Bump version and update NEWS by
const-ae <artjom31415@googlemail.com>2021-07-01 13:47:23 +0200;
8ed7ba3 Fix bug in estimate_betas_optim if ridge penalty was set by
const-ae <artjom31415@googlemail.com>2021-07-01 13:46:44 +0200;
cb3b103 estimate_beta_optim returns NA's if optim doesn't converge by
const-ae <artjom31415@googlemail.com>2021-07-01 13:32:57 +0200;
d670778 Clean up partial argument matching by
const-ae <artjom31415@googlemail.com>2021-07-01 11:59:54 +0200;
327ac27 Fix some broken tests by
const-ae <artjom31415@googlemail.com>2021-07-01 11:46:16 +0200;
e1623e7 Add estimate_betas_optim as fallback if estimate_betas_fisher_scoring fails by
const-ae <artjom31415@googlemail.com>2021-06-30 19:09:46 +0200;
bf89675 Refactor warn_non_convergence by
const-ae <artjom31415@googlemail.com>2021-06-30 18:22:30 +0200;
fa249d9 Start making glm_gp robust against accidental internal NA's by
const-ae <artjom31415@googlemail.com>2021-06-30 17:14:43 +0200;
5a5e68e Bump version and update news by
const-ae <artjom31415@googlemail.com>2021-06-22 16:12:19 +0200;
fa40d0b Update NEWS for version 1.4 by
const-ae <artjom31415@googlemail.com>2021-06-22 16:11:43 +0200;
31f7655 Choose a more reasonable scale for global overdispersion estimate by
const-ae <artjom31415@googlemail.com>2021-06-22 16:10:18 +0200;
71f5115 Add tests for matrix contrasts by
const-ae <artjom31415@googlemail.com>2021-05-26 18:08:19 +0200;
b720867 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 16:51:11 +0000;
908a0c3 (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 16:51:11 +0000;
844c451 Update NEWS and bump version by
const-ae <artjom31415@googlemail.com>2021-04-27 23:06:54 +0200;
8b727f5 Force conversion to dense if on_disk is explicitly set by
const-ae <artjom31415@googlemail.com>2021-04-27 23:05:51 +0200;
6c5c931 Update NEWS and bump version by
const-ae <artjom31415@googlemail.com>2021-04-01 11:39:23 +0200;
fa4d1c7 Fix bug in residual calculation by
const-ae <artjom31415@googlemail.com>2021-04-01 11:38:24 +0200;
367e010 Update NEWS and bump version by
const-ae <artjom31415@googlemail.com>2021-04-01 11:35:04 +0200;
f95f49a Update README by
const-ae <artjom31415@googlemail.com>2021-03-19 16:06:47 +0100;
7594edb Merge branch 'regularization' by
const-ae <artjom31415@googlemail.com>2021-03-19 15:51:42 +0100;
66f57fc Make sure that residuals are pristine and named by
const-ae <artjom31415@googlemail.com>2021-03-19 15:19:34 +0100;
ecf8390 Move potentially long output to end of error message to avoid truncation by
const-ae <artjom31415@googlemail.com>2021-02-23 16:16:25 +0100;
c3a356e Update documentation by
const-ae <artjom31415@googlemail.com>2021-02-22 12:07:33 +0100;
b630c9f Update README by
const-ae <artjom31415@googlemail.com>2021-02-22 11:32:17 +0100;
d1c0ddc Use summed deviance instead of mean deviance again by
const-ae <artjom31415@googlemail.com>2021-02-22 11:07:29 +0100;
d80d77b Apply ridge penalty to diagonal of tikhonov matrix and scale penalty by number of rows by
const-ae <artjom31415@googlemail.com>2021-02-22 10:42:02 +0100;
4257261 Penalizeation: make sure that type of matrix square root doesn't affect result by
const-ae <artjom31415@googlemail.com>2021-02-19 18:37:49 +0100;
f67d305 Add Acknowlegments section to README by
const-ae <artjom31415@googlemail.com>2021-02-16 15:39:33 +0100;
55057cb If size_factors = TRUE, use deconvolution only if scran is installed by
const-ae <artjom31415@googlemail.com>2021-02-08 10:32:47 +0100;
8199de4 Fix typos (#18) by
const-ae <artjom31415@googlemail.com>2021-02-05 17:48:25 +0100;
c07c5ba Fix botched rebase :/ by
const-ae <artjom31415@googlemail.com>2021-01-23 15:28:52 +0100;
1d2c0f9 Add option to specify the target value for beta via ridge_penalty attr by
const-ae <artjom31415@googlemail.com>2021-01-23 15:16:04 +0100;
