1. batchelor
  2. Graph
Graph of batchelor
  • *
  • *
  • *
  • *
  • *
  • *
  • | *
  • * |
  • * |
  • |/
  • *
  • | *
  • | |\
  • | |/
  • |/|
  • * |
  • | *
  • | |\
  • | |/
  • |/|
  • * |
  • | *
  • * |
  • * |
  • |/
  • *
  • *
  • *
  • | *
  • * |
  • | *
  • * |
  • * |
  • |/
  • *
  • *
  • *
  • *
  • | *
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • | *
  • * |
  • | *
  • | *
  • * |
  • * |
  • * |
  • * |
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • 22f45ec (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 11:12:24 -0400;
  • 7372827 (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 11:12:24 -0400;
  • 45d6bd9 Handle custom level ordering in batch= factor with tree-like weights. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2023-07-11 16:58:27 -0700;
  • 0a15bbf Avoid warnings due to updates to MatrixStats name defaults. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2023-06-30 11:22:34 -0700;
  • 4675c3a 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;