Bioconductor Code: Browse

Graph ofvelociraptor

7ac0199 (HEAD -> master, origin/master, origin/HEAD) 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 11:22:57 -0400;
97efe6b (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 <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:22:57 -0400;
0ee7651 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 16:08:47 +0000;
3a7545b (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 16:08:47 +0000;
22bad42 Switch zellkonverter::.AnnDataDependencies to zellkonverter::AnnDataDependencies() (#60) by Charlotte Soneson <charlottesoneson@gmail.com> 2022-04-21 09:57:38 +0200;
b1e1ad1 Merge branch 'master' of git.bioconductor.org:packages/velociraptor by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2022-02-04 09:36:53 +0000;
739437d Remove column names of reduced dimension representation (#58) by Charlotte Soneson <charlottesoneson@gmail.com> 2022-02-04 10:36:01 +0100;
7343fc3 Starting with BioC 3.15 + R 4.2, 32-bit Windows is no longer supported so Windows builds are single arch only (i.e. 64-bit only) by Hervé Pagès <hpages.on.github@gmail.com> 2021-12-16 12:42:53 -0800;
2a59b9c add example for scvelo.params argument (#57) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-12-14 10:21:37 +0000;
fbca88c 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 17:03:06 +0000;
ca6d3dc (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 17:03:06 +0000;
635dbaf Add typing extensions (#54) by Charlotte Soneson <charlottesoneson@gmail.com> 2021-10-25 16:34:58 +0200;
d61b78d Update github action (#48) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-08-13 13:11:37 +0100;
2dc89ca 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 16:55:56 +0000;
3e78025 (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 16:55:56 +0000;
3cc70ae Move sanity check vignette to inst/ (#45) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-02-26 13:24:25 +0000;
d7298ef Disable Pkgdown and docker to cache packages on successful run (#44) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-02-25 16:01:40 +0000;
ac6f739 Build and deploy Docker image from GitHub Actions to DockerHub (#43) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-02-23 10:50:33 +0000;
99b79f4 Use biocthis template for GitHub Actions (#42) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-02-22 21:44:22 +0000;
9f0ccb0 add Michael Stadler to package authors (#41) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-02-22 13:31:04 +0000;
6509bc0 Update scvelo.R (#33) by Federico Marini <marinif@uni-mainz.de> 2021-02-22 12:24:10 +0100;
993b235 Add sanity check (pkgdown-enabled) (#37) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-02-22 09:40:39 +0000;
d72ccc5 prepare release 1.1.2 (#38) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-02-21 19:32:41 +0000;
229fea0 Add plotting functions to visualize RNA velocities (#30) by Michael Stadler <stadler.michael@gmail.com> 2021-02-21 12:55:35 +0100;
0b02342 version bump to refresh cached environment (#36) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2021-02-08 14:08:54 +0000;
7d40eba Minor vignette rewording. by Aaron Lun <lun.aaron@gene.com> 2021-02-03 08:42:38 -0800;
8ec54c1 replace TVTB badges/links with velociraptor ones (#25) by Tim Triche, Jr <tim.triche@gmail.com> 2020-11-17 12:23:05 -0500;
7afbccc Update installation instructions in README (#24) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-11-04 15:18:09 +0000;
105b7c1 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 12:01:39 -0400;
7cd4624 (origin/RELEASE_3_12, RELEASE_3_12) 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 12:01:39 -0400;
49fbf28 Convert functions to S4 methods for SCE dispatch, closes #23. Minor variable renaming to avoid confusion. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-10-10 21:48:08 -0700;
4845886 add empty line to force cache update by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-28 17:44:23 +0100;
2c7ac7d 0.99.7 force cache update in attempt to get rid of outdated warning by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-28 17:18:46 +0100;
4ed2f0f 0.99.6 autoscale=FALSE by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-28 16:36:07 +0100;
6c77d82 0.99.5 to trigger new build by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-28 15:32:05 +0100;
1390e18 Update README.md by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-28 15:16:49 +0100;
1af9014 Trigger new build to check whether TIMEOUT issue on Windows is reproducible. (#22) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-21 17:01:43 +0100;
d3d6539 Explicitly declare all scvelo dependencies (#21) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-13 23:56:19 +0100;
a624b64 Add hexsticker (#20) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-13 10:35:08 +0100;
0315490 version 0.99.1 (#19) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-11 21:52:01 +0100;
81460e2 gitignore Rproj (#18) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-11 21:48:08 +0100;
c5816a8 move docker container to the end of the GHA (#17) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-11 09:47:48 +0100;
6d3ffb1 Fix BiocCheck and downsample dataset in vignette (#16) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-09-10 20:52:11 +0100;
4c3c4a1 Manually write and edit sysreq commands in GHA (#15) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-08-28 21:00:15 +0100;
14085e6 Clean up before Bioconductor submission (#14) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-08-25 15:26:45 +0100;
226457f Add some explanations and reference to data to the vignette (#10) by Charlotte Soneson <charlottesoneson@gmail.com> 2020-07-29 21:33:01 +0200;
7c83016 Added some basic tests for embedding functions. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-25 23:07:00 -0700;
bb34624 Reoxygenated. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-25 22:48:35 -0700;
3cd8eea Added the t-SNE plus embedded arrows into the user's guide. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-25 22:48:16 -0700;
4c5922c Added a utility to compact velocity vectors into a grid. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-25 22:41:39 -0700;
0d6ab0d Added the embedVelocity wrapper, which does what it says. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-25 21:16:21 -0700;
4cfac74 Try installing zellkonverter first. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-24 22:07:29 -0700;
50dd097 Piggy-back off zellkonverter's dependency list. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-24 22:04:56 -0700;
7177efa Added vignette and extra Suggests for the demonstration. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-24 22:00:51 -0700;
851a697 Added zellkonverter to the installation workflow. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-24 21:16:03 -0700;
8f9ca6f Bugfix for correct SCE dimred passing. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-24 21:01:47 -0700;
0fee89d Added perfunctory tests for the scvelo pipeline. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-24 21:01:19 -0700;
5f3e920 Switch to using zellkonverter for AnnData conversion. Minor documentation clean-ups for output description. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-24 20:23:58 -0700;
a1b44f2 Fix deployment to gh-pages using latest git (#7) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-06-21 23:10:51 +0100;
a4352cd Slight rewording on ambiguous reads. (#6) by Charlotte Soneson <charlottesoneson@gmail.com> 2020-06-16 20:15:23 +0200;
d921284 Added Matrix as an Imports. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-16 00:24:28 -0700;
7fdfe2e Reoxygenated, added Charlotte to authors. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-15 23:49:33 -0700;
1b03f83 Minor fixes and cleanup. Fleshed out manual docs. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-15 23:48:56 -0700;
77e0d06 Disambiguate 'x' (argument name) from 'X' (AnnData matrix). by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-15 23:27:31 -0700;
dff9e84 Removed unnecessarily explicit arguments in S(C)E methods. More fleshing out of the docs. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-15 22:28:01 -0700;
64c41b1 Reorganized documentation, added citation. Removed useless compliance to 80-char limit. Minor refactoring of how dimreds are handled for S(C)Es. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-15 22:15:33 -0700;
c4ba96f Stripped out largely unnecessary normalization option. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-15 21:42:28 -0700;
fdaee79 Add x matrix to use for dimension reduction by Charlotte Soneson <charlottesoneson@gmail.com> 2020-06-14 21:13:39 +0200;
ff3aea0 setMethod for SCE by Charlotte Soneson <charlottesoneson@gmail.com> 2020-06-10 21:03:20 +0200;
6737175 docfixes, remove neighbor calculations by Charlotte Soneson <charlottesoneson@gmail.com> 2020-06-10 20:23:57 +0200;
1aa0b7d Initial support for nearest neighbors via BiocNeighbors by Charlotte Soneson <charlottesoneson@gmail.com> 2020-06-10 11:45:09 +0200;
09792a6 Allow scVelo function arguments to be provided by Charlotte Soneson <charlottesoneson@gmail.com> 2020-06-08 16:26:34 +0200;
6f20458 scVelo does not log-transform normalized counts by Charlotte Soneson <charlottesoneson@gmail.com> 2020-06-08 16:06:05 +0200;
0356410 AnnData is transposed compared to SCE by Charlotte Soneson <charlottesoneson@gmail.com> 2020-06-08 15:55:39 +0200;
ac08cfd Add github action (#2) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-06-07 12:21:50 +0100;
183d4cb Return an SE with all the velocity-related statistics. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-05 00:06:02 -0700;
fb1c77a Reoxygenated. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-04 22:08:04 -0700;
5205b2b Updated all the imports. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-04 22:06:58 -0700;
0e29282 Coerce inputs to dgCMatrix or ordinary matrices. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-04 22:06:20 -0700;
262805d Control normalization and gene selection unless specified otherwise. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-04 21:53:37 -0700;
3ad0dcf Added various other imports, reoxygenated. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-04 21:13:22 -0700;
20fa457 Added stub function to run scvelo. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-04 21:12:59 -0700;
cae6cc2 Added various tidbits required to get basilisk to run. by LTLA <infinite.monkeys.with.keyboards@gmail.com> 2020-06-04 20:38:12 -0700;
1882788 add package doc (autogenerated from DESCRIPTION) by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-06-04 08:56:06 +0100;
7b6901a Add GitHub links to DESCRIPTION by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-06-04 08:49:54 +0100;
7d0315f Initial commit by Kevin Rue-Albrecht <kevinrue67@gmail.com> 2020-06-04 08:49:26 +0100;