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08 March 2025, 10:38:43 UTC
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8d89492 Matthew D. Young01 November 2022, 13:12:09 UTCMerge pull request #122 from constantAmateur/devel Devel01 November 2022, 13:12:09 UTC
7341e8f Matthew Young01 November 2022, 13:03:21 UTCFix Matrix calls01 November 2022, 13:03:21 UTC
28dbb60 Matthew Young01 September 2022, 10:14:52 UTCAttempt at fix for V7 cellranger folder structure change.01 September 2022, 10:14:52 UTC
fb585e3 Matthew D. Young26 May 2022, 09:24:47 UTCMerge pull request #112 from constantAmateur/devel Fixed vignette and package size issue.26 May 2022, 09:24:47 UTC
d0694a2 Matthew Young26 May 2022, 09:24:09 UTCFixed vignette and package size issue.26 May 2022, 09:24:09 UTC
3cce5fb Matthew D. Young24 May 2022, 14:27:56 UTCUpdate README.md24 May 2022, 14:27:56 UTC
67cdd85 Matthew D. Young24 May 2022, 14:26:32 UTCMerge pull request #111 from constantAmateur/devel Devel24 May 2022, 14:26:32 UTC
68de997 Matthew Young24 May 2022, 14:21:02 UTC1.6.0 - Added some checks and security around setting of clusters with `setClusters`. - Add warnings and extra documentation about library complexity to `autoEstCont`. - Fix pointSize bug in plotting function. - Merge pull adding support for multi.24 May 2022, 14:21:02 UTC
1800912 Matthew D. Young24 May 2022, 12:24:41 UTCMerge pull request #91 from maxim-h/devel Add support for cellranger-arc output.24 May 2022, 12:24:41 UTC
d345f17 kholmato19 October 2021, 12:31:41 UTCAdd support for cellranger-arc output19 October 2021, 12:31:41 UTC
d0c061d Matthew D. Young14 May 2021, 13:06:39 UTCMerge pull request #82 from constantAmateur/devel Fix CRAN submission issues.14 May 2021, 13:06:39 UTC
3e4d50d Matthew Young14 May 2021, 13:05:40 UTCFix CRAN submission issues.14 May 2021, 13:05:40 UTC
0302773 Matthew D. Young13 May 2021, 08:36:05 UTCUpdate README.md Fix vignette link.13 May 2021, 08:36:05 UTC
204b602 Matthew D. Young13 May 2021, 08:33:58 UTCMerge pull request #81 from constantAmateur/devel Devel13 May 2021, 08:33:58 UTC
4699873 Matthew Young13 May 2021, 08:31:19 UTCMerge branch 'devel' of https://github.com/constantAmateur/SoupX into devel13 May 2021, 08:31:19 UTC
6409c78 Matthew Young13 May 2021, 08:30:54 UTCAdded check for compatability of toc/tod, more info in autoEstCont output, and fix cran compression thing.13 May 2021, 08:30:54 UTC
bf52dd9 Matthew D. Young14 January 2021, 08:19:44 UTCUpdate README.md Link to CRAN vignette.14 January 2021, 08:19:44 UTC
f4c1e43 Matthew D. Young13 January 2021, 11:18:21 UTCMerge pull request #68 from constantAmateur/devel Update load10X13 January 2021, 11:18:21 UTC
9af7f71 Matthew D. Young13 January 2021, 11:18:08 UTCMerge branch 'master' into devel13 January 2021, 11:18:08 UTC
6754c4a Matthew Young13 January 2021, 10:54:56 UTCUpdate load10X13 January 2021, 10:54:56 UTC
592bcc3 Matthew D. Young15 October 2020, 08:45:31 UTCUpdate README.md15 October 2020, 08:45:31 UTC
6be48cd Matthew D. Young15 October 2020, 08:44:14 UTCMerge pull request #58 from constantAmateur/devel Further vignette fixes.15 October 2020, 08:44:14 UTC
4b7a520 Matthew Young15 October 2020, 08:43:38 UTCFurther vignette fixes.15 October 2020, 08:43:38 UTC
9d70f3c Matthew D. Young15 October 2020, 07:20:19 UTCUpdate README.md15 October 2020, 07:20:19 UTC
558a0e5 Matthew D. Young15 October 2020, 07:19:16 UTCMerge pull request #57 from constantAmateur/devel Fix links in vignette.15 October 2020, 07:19:16 UTC
b9c388d Matthew Young15 October 2020, 07:18:50 UTCFix links in vignette.15 October 2020, 07:18:50 UTC
7c40ce0 Matthew D. Young14 October 2020, 15:46:04 UTCUpdate README.md Update vignette link.14 October 2020, 15:46:04 UTC
bcc7c3f Matthew D. Young14 October 2020, 15:41:25 UTCMerge pull request #56 from constantAmateur/devel Devel14 October 2020, 15:41:25 UTC
95d3848 Matthew Young14 October 2020, 15:39:47 UTCPrep for release.14 October 2020, 15:39:47 UTC
c3f8feb Matthew Young14 October 2020, 15:31:36 UTCCleanup14 October 2020, 15:31:36 UTC
1ba2389 Matthew Young14 October 2020, 15:17:25 UTCFix some conflicts.14 October 2020, 15:17:25 UTC
04e3ab0 Matthew Young14 October 2020, 15:07:07 UTCAdd vignette build.14 October 2020, 15:07:07 UTC
867c142 Matthew Young14 October 2020, 14:10:34 UTCNew plot options, updated vignette.14 October 2020, 14:10:34 UTC
61d3350 Matthew D. Young06 July 2020, 08:24:00 UTCUpdate README.md Fix vignette link to new version.06 July 2020, 08:24:00 UTC
63674d4 constantAmateur06 July 2020, 08:21:30 UTCUpdate vignette.06 July 2020, 08:21:30 UTC
792a681 Matthew D. Young06 July 2020, 07:53:13 UTCMerge pull request #48 from yihui/patch-1 Suggest formatR because of the chunk option tidy=TRUE in the vignette06 July 2020, 07:53:13 UTC
7f2503a Yihui Xie17 June 2020, 03:44:03 UTCSuggest formatR because of the chunk option tidy=TRUE in the vignette This will fix the warnings about formatR on CRAN: https://cran.r-project.org/web/checks/check_results_SoupX.html17 June 2020, 03:44:03 UTC
572a0cd Matthew Young27 May 2020, 12:25:31 UTCAdd vignette build.27 May 2020, 12:25:31 UTC
eabd201 Matthew Young27 May 2020, 12:15:19 UTCFirst CRAN release.27 May 2020, 12:15:19 UTC
ecd4441 Matthew Young27 May 2020, 12:07:30 UTCCRAN initial release.27 May 2020, 12:07:30 UTC
a01ddb0 Matthew Young15 May 2020, 16:34:34 UTCSub-sample PBMC data to meet CRAN file size requirements.15 May 2020, 16:34:34 UTC
8ce9f8b Matthew Young15 May 2020, 15:24:10 UTCcompression test 215 May 2020, 15:24:10 UTC
b257b02 Matthew Young15 May 2020, 15:15:55 UTCCompression test.15 May 2020, 15:15:55 UTC
485f73b Matthew Young15 May 2020, 12:32:56 UTCA few typos and minor syntax fixes15 May 2020, 12:32:56 UTC
c18cd2a Matthew Young14 May 2020, 20:34:43 UTCRemove dependence of downloading in vignette. Switch back to dontrun.14 May 2020, 20:34:43 UTC
09599af Matthew Young14 May 2020, 10:59:20 UTCSome fixes.14 May 2020, 10:59:20 UTC
02e9266 Matthew Young14 May 2020, 10:41:17 UTCAnother restructure of vignette and data.14 May 2020, 10:41:17 UTC
dd6e4c1 Matthew Young10 May 2020, 22:50:38 UTCUpdate vignette.10 May 2020, 22:50:38 UTC
2f30dfb Matthew Young10 May 2020, 22:45:57 UTCAdd toy data and live examples.10 May 2020, 22:45:57 UTC
1a85d86 Matthew Young06 May 2020, 20:00:14 UTCAdd examples to documentation.06 May 2020, 20:00:14 UTC
04f9060 Matthew Young05 May 2020, 22:58:07 UTCSplit data into one RData file per object as required. Enable lazy loading.05 May 2020, 22:58:07 UTC
b5096d9 Matthew Young05 May 2020, 11:09:33 UTCUpdated data object.05 May 2020, 11:09:33 UTC
e2fcd2b Matthew Young05 May 2020, 11:03:10 UTCReformulation using github as source for tod.05 May 2020, 11:03:10 UTC
e10ff69 Matthew Young05 May 2020, 10:36:02 UTCAnother attempt at data loading without including in package.05 May 2020, 10:36:02 UTC
0521271 Matthew Young05 May 2020, 10:28:16 UTCChange vignette data source.05 May 2020, 10:28:16 UTC
4955824 Matthew Young05 May 2020, 10:11:24 UTCAdd raw data.05 May 2020, 10:11:24 UTC
8325cda Matthew Young05 May 2020, 07:37:35 UTCFix bug with cell weighting in expansion routine.05 May 2020, 07:37:35 UTC
55158e9 Matthew Young05 May 2020, 07:35:22 UTCAdd CRAN related cruft.05 May 2020, 07:35:22 UTC
2f5553c Matthew Young05 May 2020, 07:26:52 UTCSpelling fixes.05 May 2020, 07:26:52 UTC
c0b0d4d Matthew Young04 May 2020, 23:47:23 UTCAlter vignette to meet CRAN file size requirements. Add helper function to set soup profile manually. Some other minor tweaks.04 May 2020, 23:47:23 UTC
228864e Matthew Young04 May 2020, 10:41:07 UTCTransition cluster expansion to much faster closed form routine instead of iteration.04 May 2020, 10:41:07 UTC
548e491 Matthew Young01 May 2020, 23:45:55 UTCCompletely remove all inline backticks. Escape dollars, which might be cause as well01 May 2020, 23:45:55 UTC
825451b Matthew Young01 May 2020, 17:20:36 UTCAnother attempt at CRAN fixes.01 May 2020, 17:20:36 UTC
9398603 Matthew Young30 April 2020, 22:14:15 UTCStop autoEstCont using an absurd number of genes. Attempt to fix windows build error on vignette for CRAN.30 April 2020, 22:14:15 UTC
773e844 Matthew Young30 April 2020, 15:48:30 UTCMigrate from rawgit30 April 2020, 15:48:30 UTC
650f7fa Matthew Young30 April 2020, 15:43:31 UTCAdd built vignette.30 April 2020, 15:43:31 UTC
460412e Matthew D. Young30 April 2020, 15:37:40 UTCMerge pull request #43 from constantAmateur/devel Devel30 April 2020, 15:37:40 UTC
052121f Matthew D. Young30 April 2020, 15:37:20 UTCMerge branch 'master' into devel30 April 2020, 15:37:20 UTC
83f49fd Matthew Young30 April 2020, 15:18:25 UTCUpdated data object so vignette doesn't depend on wget. A number of other small fixes.30 April 2020, 15:18:25 UTC
f6eb86f Matthew Young28 April 2020, 09:06:17 UTCVarious fixes to clean up R CMD check.28 April 2020, 09:06:17 UTC
f6bb349 Matthew Young27 April 2020, 13:53:07 UTCA few fixes and vignette update.27 April 2020, 13:53:07 UTC
88a4dee Matthew Young22 April 2020, 13:06:34 UTCRemove non-ascii characters from plotting function.22 April 2020, 13:06:34 UTC
7c2580f Matthew Young15 April 2020, 14:07:36 UTCAdd warnings and sanity checks to auto-estimation. Improve defaults.15 April 2020, 14:07:36 UTC
1d7d8fd Matthew D. Young28 February 2020, 20:04:41 UTCMerge pull request #34 from gtca/master Fix matrix subsetting in expandClusters28 February 2020, 20:04:41 UTC
d45cae1 gtca26 February 2020, 12:53:13 UTCFix matrix subsetting in expandClusters Due to automatic matrix -> numeric conversion in R, if a cluster with only one cell was present, expandClusters() was failing.26 February 2020, 12:53:13 UTC
a344b71 Matthew Young17 February 2020, 08:52:23 UTCDocumentation fix.17 February 2020, 08:52:23 UTC
1f6c0fb Matthew Young05 February 2020, 12:42:55 UTCBugfixes and version number update.05 February 2020, 12:42:55 UTC
f78e480 Matthew Young05 February 2020, 11:02:23 UTCDocumentation fix.05 February 2020, 11:02:23 UTC
b19195f Matthew Young03 February 2020, 19:37:50 UTCFixed some auto mode bugs.03 February 2020, 19:37:50 UTC
aef7126 Matthew D. Young03 February 2020, 14:02:04 UTCMerge pull request #29 from constantAmateur/devel Devel03 February 2020, 14:02:04 UTC
b67f13f Matthew Young03 February 2020, 13:17:31 UTCAdjust gitignore03 February 2020, 13:17:31 UTC
ddf8497 Matthew Young03 February 2020, 13:16:59 UTCAdd vignette build.03 February 2020, 13:16:59 UTC
89e06c4 Matthew Young03 February 2020, 12:37:49 UTCBug fixes, parallel adjust and increase cluster focus.03 February 2020, 12:37:49 UTC
d7c58f7 Matthew D. Young20 January 2020, 09:09:42 UTCUpdate README.md Add note about multtest issue.20 January 2020, 09:09:42 UTC
01558a4 Matthew Young02 December 2019, 14:48:58 UTCMerge branch 'master' of https://github.com/constantAmateur/SoupX02 December 2019, 14:48:58 UTC
18d7152 Matthew Young02 December 2019, 14:48:46 UTCFixed bug where no change in transcription (-Inf on log scale) was plotted as NA02 December 2019, 14:48:46 UTC
ad9562f Matthew Young02 December 2019, 14:48:19 UTCFixed bug where no change in transcription (-Inf on log scale) was plotted as NA02 December 2019, 14:48:19 UTC
89386dd Matthew D. Young25 November 2019, 10:29:29 UTCUpdate README.md Fix link to vignette.25 November 2019, 10:29:29 UTC
342266c Matthew Young25 November 2019, 09:36:17 UTCMajor rework of code to simplify method.25 November 2019, 09:36:17 UTC
a3354be Matthew Young13 April 2019, 12:19:34 UTCUpdate load functions for cellranger v3.0.0 compatability13 April 2019, 12:19:34 UTC
549f8de Matthew D. Young14 July 2018, 20:20:03 UTCMerge pull request #4 from mschilli87/patch-1 Fix link to paper in README.14 July 2018, 20:20:03 UTC
76e56ec Marcel Schilling03 July 2018, 13:03:00 UTCFix link to paper in README Instead of linking to the paper, the README refenced the github repository itself. This commit fixes this by referencing the DOI of the SoupX pre-print instead.03 July 2018, 13:03:00 UTC
348e05a Matthew D. Young20 June 2018, 10:45:22 UTCUpdate README.md20 June 2018, 10:45:22 UTC
3f2425c Matthew Young20 June 2018, 10:41:01 UTCImproved interpolation, plotting and documentation. Some bug fixes.20 June 2018, 10:41:01 UTC
388cc08 Matthew Young11 June 2018, 11:19:00 UTCVersion update. Lowess smoothing, single channel processing options.11 June 2018, 11:19:00 UTC
226e7a2 Matthew D. Young16 May 2018, 20:48:59 UTCUpdate README.md16 May 2018, 20:48:59 UTC
f815b57 Matthew Young16 May 2018, 15:46:45 UTCMerge branch 'master' of github.com:constantAmateur/SoupX16 May 2018, 15:46:45 UTC
0f8ab4c Matthew Young16 May 2018, 15:46:32 UTCVersion update to 0.2.216 May 2018, 15:46:32 UTC
d9918fe Matthew D. Young13 May 2018, 19:09:10 UTCUpdate README.md13 May 2018, 19:09:10 UTC
15248c9 Matthew D. Young13 May 2018, 19:08:21 UTCUpdate README.md Fix link13 May 2018, 19:08:21 UTC
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