- batchelor
- Graph
-
4675c3a
(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 11:09:01 -0400;
-
8ecc91e
(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 11:09:01 -0400;
-
a1f3e84
(origin/RELEASE_3_16, RELEASE_3_16)
Report full rownames when correct.all=TRUE in mnnCorrect. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2023-01-03 12:16:37 +1100;
-
59e325a
Report full rownames when correct.all=TRUE in mnnCorrect. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2023-01-03 12:16:37 +1100;
-
99400d0
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 11:19:32 -0400;
-
-
a5912c3
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 11:19:32 -0400;
-
94788f9
(origin/RELEASE_3_15, RELEASE_3_15)
Merge branch 'master' into RELEASE_3_15 by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2022-06-22 09:41:21 -0700;
-
-
-
-
b2568a2
Tougher checks on the length of the batch= argument. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2022-06-22 09:40:35 -0700;
-
69d4ed5
Merge branch 'master' into RELEASE_3_15 by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2022-06-21 21:05:40 -0700;
-
-
-
-
6a93c97
Set rownames on the combined rowData for character subset.row=. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2022-06-21 20:49:53 -0700;
-
685db2e
Avoid issues with subsetting via do.call. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2022-05-25 16:05:46 -0700;
-
51f8b0b
Avoid issues with subsetting via do.call, fixes #32. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2022-05-25 16:05:46 -0700;
-
d366583
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 15:54:12 +0000;
-
-
b5ab993
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 15:54:12 +0000;
-
be310ee
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 16:50:33 +0000;
-
fbbcf91
(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 16:50:33 +0000;
-
ac1b37a
(origin/RELEASE_3_13, RELEASE_3_13)
quickCorrect returns all genes by default after correcting on HVGs. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-08-11 00:12:38 -0700;
-
ea09e98
quickCorrect returns all genes by default after correcting on HVGs. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-08-11 00:12:38 -0700;
-
da09d7e
Actually use the HVGs in quickCorrect. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-08-11 00:00:51 -0700;
-
7d3d3ab
Actually use the HVGs in quickCorrect. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-08-11 00:00:51 -0700;
-
eb244bd
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 16:42:21 +0000;
-
-
58f6f51
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 16:42:21 +0000;
-
f2af3ba
Minor doc update. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-05-11 22:17:16 -0700;
-
ea913b6
Realize file-backed matrices prior to PCA. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-05-11 22:15:51 -0700;
-
0fca00a
Updated test for fixed dqrng seed issue. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-05-11 21:57:20 -0700;
-
b108a53
(origin/RELEASE_3_12, RELEASE_3_12)
Added rmarkdown as a suggests. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-04-16 00:26:43 -0700;
-
90bd946
Added rmarkdown as a suggests. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-04-16 00:26:43 -0700;
-
4f0a45a
Mention treatment of factors in merge.order's leaves. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-04-06 23:57:39 -0700;
-
fc7a894
Added more factor-related tests out of paranoia. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-04-06 23:52:48 -0700;
-
9630957
Reoxygenated, bumped version and date. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-04-06 23:04:42 -0700;
-
e3331a0
Correctly handle factors in the merge order. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-04-06 21:24:14 -0700;
-
87b6c06
Migrated cluster comparison function to bluster. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-04-05 19:09:04 -0700;
-
541f282
Added a few cluster-based diagnostics from the book. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-04-05 16:09:43 -0700;
-
853b579
Bumped version, date; updated NEWS. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-03-06 19:36:54 -0800;
-
3b4b03a
Bugfix for test for the time being. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-03-06 19:36:05 -0800;
-
6cda26c
Added a whole stack of files to .gitignore. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-03-06 00:14:17 -0800;
-
d471093
Removed accidentally committed file. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-03-06 00:13:24 -0800;
-
d90d744
Bugfixes and tests for the new quickCorrect function. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-03-05 23:55:59 -0800;
-
ccc6693
Added a quickCorrect function to wrap the usual workflow. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-03-04 23:58:25 -0800;
-
052656a
Added utility to quickly intersect the rows. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-03-04 22:58:58 -0800;
-
b03fc92
Use the variance of MNN deltas as a correction diagnostic (#28). by
Aaron Lun <LTLA@users.noreply.github.com>
2021-03-03 23:34:44 -0800;
-
f384fa3
Bumped version and date. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-02-02 22:30:36 -0800;
-
11f8b6e
Minor example clean-up. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-29 22:42:56 -0800;
-
be6ba6b
Exported the PC->SCE converter. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-29 22:04:42 -0800;
-
2321772
Added the applyMultiSCE to easily handle alternative Exps. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-27 23:59:05 -0800;
-
a4655a9
Removed as.altexp= in favor of SingleCellExperiment::applySCE. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-27 23:28:28 -0800;
-
cca6d53
Clarified d=NA in docs. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-23 02:33:30 -0800;
-
e013323
Bugfix to handling of d=NA with subset.row= in fastMNN. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-23 02:26:56 -0800;
-
02e60c3
Support d=NA in multiBatchPCA. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-23 02:04:33 -0800;
-
0ffadd7
Bumped version and date, updated NEWS. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-21 22:45:01 -0800;
-
bca2422
Added as.altexp= for multiBatchPCA. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-21 22:44:47 -0800;
-
989145d
Added an as.altexp= option to easily run on altexps. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-21 22:27:11 -0800;
-
f09c8e8
Minor refactoring, reordered arguments for multiBatchNorm. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-21 20:49:02 -0800;
-
f042e92
More convenient support for alternative Experiments in multiBatchNorm. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-20 22:57:33 -0800;
-
b36397b
Replaced DeferredMatrix with the new ScaledMatrix. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2021-01-11 21:31:48 -0800;
-
9d04a87
Migrate findMutualNN to BiocNeighbors. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-12-05 15:27:00 -0800;
-
56b8c5f
Improved the error message for checkBatchConsistency. Closes #22. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-11-25 21:02:40 -0800;
-
7860135
Improved the error message for checkBatchConsistency. Closes #22. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-11-25 21:02:40 -0800;
-
92b6b86
Bumped version and date. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-11-16 21:06:09 -0800;
-
2ac8384
Protect against accidental naming from DF arguments. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-11-16 20:49:59 -0800;
-
cdf0970
Bumped version and date. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-11-16 21:01:54 -0800;
-
806c865
Protect against accidental naming from DF arguments. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-11-16 20:49:59 -0800;
-
3477797
Switched to S4Vectors::I. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-11-07 16:42:14 -0800;
-
2b32941
bump x.y.z version to odd y following creation of RELEASE_3_12 branch by
Nitesh Turaga <nitesh.turaga@gmail.com>
2020-10-27 11:44:25 -0400;
-
-
45979b4
bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by
Nitesh Turaga <nitesh.turaga@gmail.com>
2020-10-27 11:44:25 -0400;
-
1e11cb2
reducedMNN now unpacks input lists. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-10-24 01:45:27 -0700;
-
e454adc
Imbue clusterMNN with the ability to do its own clustering. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-10-24 00:07:09 -0700;
-
930b5ef
Define batch when only design= is specified in regressBatches. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-10-22 00:25:39 -0700;
-
eeeb770
Bumped version and date, updated NEWS; minor docfix. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-10-17 17:06:22 -0700;
-
71bbc5b
Added PCA option to regressBatches for convenience. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-10-17 17:05:33 -0700;
-
921c7f1
Force use of deferred PCA by default in fastMNN, multiBatchPCA. Switch to Irlba as the default multiBatchPCA algorithm. Updated tests to use ExactParam, as per previous default. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-10-17 15:25:04 -0700;
-
719f63a
Bumped version and date. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-10-05 21:24:35 -0700;
-
f831a38
Abandon futile handling of non-native matrices in mnnCorrect. Simplify C++ by eliminating dependency on beachmat. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-09-26 22:25:41 -0700;
-
c71f076
Cleaned up the vignette, mention function levels. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-09-26 10:54:00 -0700;
-
b43c0f2
Streamlined regression by moving restrict logic to ResidualMatrix. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-09-26 10:29:57 -0700;
-
28d6cc9
Reoxygenated, bumped version and date, updated NEWS. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-08-21 23:32:29 -0700;
-
516df9a
Added correct.all= option to rescaleBatches, for consistency. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-08-21 23:32:11 -0700;
-
ae90342
Purged the old list unpacker to use scuttle's version. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-08-21 23:10:53 -0700;
-
8e48728
Minor docfix for more general inherited params. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-08-21 23:08:24 -0700;
-
74cfb54
Added correct.all= for consistency across correction functions. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-08-21 23:07:55 -0700;
-
61906ed
Prepend to existing single SCE in correctExpt, fixes #19. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-08-21 22:58:00 -0700;
-
35d161b
Eliminate need for batch= when design= is set in regressBatches. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-08-19 21:28:33 -0700;
-
e05a846
Minor docfix. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-07-12 01:08:02 -0700;
-
115a0f4
Bumped version and date. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-06-03 09:01:34 -0700;
-
25c8da1
Switched all imports from scater to scuttle. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-06-03 09:00:45 -0700;
-
9e8e359
bump x.y.z version to odd y following creation of RELEASE_3_11 branch by
Nitesh Turaga <nitesh.turaga@gmail.com>
2020-04-27 19:25:15 +0000;
-
cfce683
(origin/RELEASE_3_11, RELEASE_3_11)
bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by
Nitesh Turaga <nitesh.turaga@gmail.com>
2020-04-27 19:25:15 +0000;
-
5465d90
Reoxygenated, bumped version and date, updated NEWS. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-04-19 19:50:09 -0700;
-
4a24366
Preserve non-conflicting rowData in correctExperiments. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-04-19 19:26:57 -0700;
-
2273972
Minor refactoring to clarify that only size factors change. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-04-19 18:31:53 -0700;
-
0360fe0
Bumped version, date; updated NEWS; reoxygenated. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-04-15 00:26:07 -0700;
-
bbba99d
Support d=NA mode to use matrices as-is in fastMNN. Pass get.variance=TRUE to return variances from PCA. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-04-14 21:58:43 -0700;
-
7fc813f
Bugfixes for parsing tree-based weights in PCA. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-02-16 21:59:41 -0800;
-
a54aa96
Reoxygenated, bumped version and date. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-02-14 09:35:01 -0800;
-
badd975
Yet more doc clarification about list inputs. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-02-14 09:34:41 -0800;
-
aa65200
Fleshed out docs for PCA weighting. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-02-14 09:29:31 -0800;
-
bc9a31b
Added tests for multiBatchPCA's new weighting mode. Plus bugfix for errors. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-02-14 09:13:46 -0800;
-
f5a865e
Preliminary support for tree-based weights in PCA. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-02-13 23:08:54 -0800;
-
46f3022
Updated tests for more thorough single-input checks. Testfixes to address inequality of median inverse/inverse median. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-02-12 21:52:25 -0800;
-
98acfaa
Avoid unnecessary fragmentation of a single batch for multinorm. Explicitly calculate median of inverses instead of inverse median. by
LTLA <infinite.monkeys.with.keyboards@gmail.com>
2020-02-12 21:44:42 -0800;