Bioconductor Code: Browse

Graph ofCellaRepertorium

de926ef (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 11:23:20 -0400;
5346a3b (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 11:23:20 -0400;
27c07ab bump by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-05-23 14:57:13 -0400;
a67fea2 pretty printing so vignette isn't so ugly by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-05-10 11:17:37 -0400;
c9401d2 Bump, I guess? by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-04-20 12:34:43 -0400;
cfa9d7d 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 16:10:29 +0000;
c44ca63 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 16:10:29 +0000;
133e12c Handle missing contrast names by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-05-10 10:32:14 -0400;
5a2ca29 track contrast names; better names for pairwise contrasts by ANDREW MCDAVID <andrew_mcdavid@urmc.rochester.edu> 2022-05-10 03:03:28 -0400;
abe244b 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 16:10:29 +0000;
5cf49a5 (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 16:10:29 +0000;
d17a5e7 Bump, I guess? by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-04-20 12:34:43 -0400;
1a7ddf0 Tried a bunch of stuff to try to get the tidy method found. Finally gave up and exported tidy.* Pretty sure there's a bug in R I'm hitting here... by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-04-20 12:29:41 -0400;
a363231 Example of vector stats and pairwise comps by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-04-14 21:34:32 -0500;
7e0baa4 need to refer to data for observed value xintercept now by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-04-14 21:25:05 -0500;
c540f69 Still return PermuteTest for a scalar permutation statistic, but gains `contrast` element, so invalidated test cache. by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-04-14 21:04:11 -0500;
c4d88a3 Support for vector-valued permutation statistics + contrasts therein by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2022-04-14 21:04:02 -0500;
2629f95 Merge branch 'master' of git.bioconductor.org:packages/CellaRepertorium into master by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-11-10 01:50:02 -0500;
2f16fab 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 17:04:40 +0000;
ee7f173 (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 17:04:40 +0000;
73fc076 Try out the R CMD check action. by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-09-29 14:22:39 -0400;
18eee1d Merge branch 'cland' into master by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-09-28 21:53:18 -0400;
d65d595 make cluster_permute_test into a class and fix a few check errors / warnings by ANDREW MCDAVID <andrew_mcdavid@urmc.rochester.edu> 2021-09-28 21:41:35 -0400;
dfaded1 potential speed up in cland by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-09-28 16:36:56 -0400;
b30e739 Added plotting function analogous to cluster_plot() with updated .Rd documentation with example by awagna <aaron.wagner.t@gmail.com> 2021-09-21 13:49:53 -0400;
48fc373 updated cluster_permute_test to include permuted statistic values in return list by awagna <aaron.wagner.t@gmail.com> 2021-09-14 14:59:31 -0400;
c5448c4 Bump version by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-07-29 11:17:15 -0400;
730c662 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 16:57:31 +0000;
86b7f10 (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 16:57:31 +0000;
328e977 check for fine_clustering and emit warning by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-07 10:19:40 -0400;
b3a0037 Clustering intersection, towards addressing <a href="#10">#10</a> by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-07 01:17:22 -0400;
84e5442 doc updates by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-07 01:15:48 -0400;
f4d63e4 quell a warning when it's expected. by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-07 01:15:29 -0400;
67dff52 Check for scalar cluster_pk. Mostly, vectors could be used, but some places assume scalar, generally in renaming operations. Not aware of any use case to support vectors. by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-07 01:14:37 -0400;
befdd6f Cleanup plot_clustering. More sanity checks, add packages to Suggests by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-07 01:12:34 -0400;
a8a5128 Merge branch 'master' of github.com:amcdavid/CellaRepertorium by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-06 16:21:42 -0400;
af017c5 Closes <a href="#7">#7</a> by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-06 16:19:20 -0400;
2d78ede plot_clustering.R function added (#9) by Aaron Wagner <65549470+awagna@users.noreply.github.com> 2021-04-06 10:41:14 -0400;
6fcc2b5 Merge branch 'master' of github.com:amcdavid/CellaRepertorium by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-02 14:23:15 -0400;
e7270b4 handle one-column tibbles by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-04-02 14:22:41 -0400;
0a67d27 Warnings about BiocManager::version() and valid(). by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-02-09 23:38:07 -0500;
ca5e1ae expand total_umi with cell_tbl before spreading columns by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2021-01-12 15:19:37 -0500;
ddcab24 bump by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-11-22 16:24:05 -0500;
b23e97b more care for pairing in cells with no contigs by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-11-22 16:23:14 -0500;
dd80804 Fixes <a href="#6">#6</a> by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-11-05 17:32:06 -0500;
7781b69 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 12:03:47 -0400;
4e5b113 (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 12:03:47 -0400;
7614de8 alpha not available on the graphics device of the Bioc builder by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-20 14:19:16 -0400;
13ca0fd Add overview vignette by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-19 16:33:46 -0400;
0f50c42 Clean up by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-19 16:33:37 -0400;
a78c50a fix warnings and use ccdb_join function by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-19 16:33:15 -0400;
6432de0 Expand/cleanup cdr3 clustering vignette Add cluster_plot function Add a (somewhat fragile) function to test if fine_clustering has been run. by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-19 16:32:40 -0400;
594d734 Rename cluster_name to cluster_pk (since that's what it is). by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-15 10:27:43 -0400;
6c82e73 Import from BiocGenerics so that S4Vectors makes its nrow/ncol methods properly. by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-15 10:26:35 -0400;
68099a7 cast template to data.frame by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-08 14:13:00 -0400;
6f53e95 fix a few "uninitialized objects" NOTES by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-08 14:12:27 -0400;
03f092c equalize_ccdb example by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-08 14:11:08 -0400;
c0004a9 pairing_tables uses pre-ranked contig_tbl to determine primary / secondary pairings by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-08 14:09:31 -0400;
93f7873 Change in cluster_idx 1 / cluster_idx 2 order (but it was arbitrary before because of ties). by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-07 14:38:54 -0400;
bcb0b0f Cross ref cluster_permute_test example by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-06 01:57:22 -0400;
72331ff Check class with `inherits` rather than `class` and add an example by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-06 01:56:54 -0400;
698d1fb add example to generate_pseudobulk by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-06 00:42:41 -0400;
8468d28 LazyData: false hangover by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-30 16:17:48 -0400;
33a826f Bumpity bumpity, hold on tight. by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-01 17:32:32 -0400;
c53e9d4 add NEWS.md more description to data manpages by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-01 17:11:03 -0400;
2cda42b remove pkgdown from master (will move to pkgdownExtra branch) by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-01 16:37:18 -0400;
f6fe44e Merge branch 'master' of github.com:amcdavid/CellaRepertorium by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-01 16:30:20 -0400;
8e15fec update readme by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-10-01 16:29:46 -0400;
bf34e42 explain inst/examples by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-30 15:19:15 -0400;
866b7df move data-raw to inst/script by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-30 14:47:33 -0400;
7840144 Rbuildignore WORDLIST Lazydata: FALSE Fix a few spelling errors by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-30 14:11:48 -0400;
251567b Not actually doing anything useful with the Rmd; just keep the md by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-30 13:59:08 -0400;
6534556 bioconductor installation instructions by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-30 13:58:35 -0400;
f8d9d6b Merge pull request <a href="#4">#4</a> from vonkaenelerik/master by Andrew McDavid <Andrew_McDavid@urmc.rochester.edu> 2020-09-15 13:35:16 -0400;
36ae53c Merge branch 'master' of https://github.com/vonkaenelerik/CellaRepertorium by Erik VonKaenel <vonkaenelerik@gmail.com> 2020-09-15 11:48:21 -0400;
b0f131e added ccdb_join functin with unit tests by Erik VonKaenel <vonkaenelerik@gmail.com> 2020-09-14 19:56:22 -0400;
0dd155d Maybe reduce vignette size? by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-08 17:43:52 -0400;
5928521 Remove various unused variables to quell c++ warnings by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-08 17:33:39 -0400;
608f89f Hopefully quell errors about access to functions w/o IMPORTing in BiocCheck by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-08 16:57:55 -0400;
bbbee14 Removed unused 'Swap' method (that was triggering warnings about memcpy/memset) by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-08 16:38:46 -0400;
a32b7c8 Bump version Chant a propalytic Rcpp spell (probably relating to ABI mismatches somewhere on my machine?) Check for broom.mixed (should be deprecated eventually) by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-09-03 17:17:25 -0400;
0f66836 just a dplyr attribute change by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-06-10 16:14:26 -0400;
31f54ba Fixes to handle changes in dplyr 1.0 by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-06-10 16:07:33 -0400;
d4b1933 Add a `sort` argument to deal with loss of dplyr:::all.equal.tbl_df by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-06-10 16:06:11 -0400;
a1108fa pkgdown::build_site() by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-05-18 14:33:38 -0400;
fbb51dc add function to get and color ggplot2 axes labels by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-05-18 14:23:43 -0400;
d5241b4 update pkgdown by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-01-10 14:36:47 -0500;
99d0439 bump version by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-01-08 02:08:59 -0500;
866a322 use cluster_filterset to set white_list (maybe not needed in some examples now..) by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-01-08 02:08:32 -0500;
4a2254c quell a warning from `nest` by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-01-08 01:39:44 -0500;
4275dcd Mysterious fix to get rbind to properly dispatch on ... by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-01-08 01:39:31 -0500;
1d39cfa Update calls to scater for bioc devel by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2020-01-08 00:54:48 -0500;
3257fe9 LazyData: true needed for data to be automatically in package NAMESPACE, I guess? by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2019-09-05 14:57:50 -0400;
e3b1981 bump version by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2019-09-05 14:07:19 -0400;
03b3287 Move data/manuscript prep to CellaRepertoriumData by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2019-09-05 13:53:25 -0400;
3d6037b A bit more fleshed out idea of test comparisons by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2019-09-03 14:12:37 -0400;
2b4a979 Add pseudobulk function to R/ Example script goes in inst/workflows/ by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2019-09-03 13:53:25 -0400;
8aa6f21 Merge branch 'master' of github.com:amcdavid/CellaRepertorium by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2019-09-03 12:54:37 -0400;
6296229 Shorten line length by Andrew McDavid <andrew.n.mcdavid@gmail.com> 2019-09-03 12:54:34 -0400;
b32e89b function for pseudobulk by Gu <ygu@urmc-sh.rochester.edu> 2019-09-03 12:43:06 -0400;