Skip to main content

Browse the archive

https://github.com/scverse/scanpy
12 June 2023, 04:30:47 UTC
sort by:
Revision Author Date Message Commit Date
ca1c8bb Philipp A 15 May 2018, 14:34:18 UTC require correct anndata version 15 May 2018, 14:34:18 UTC
ed9b1a4 falexwolf 15 May 2018, 12:23:04 UTC added 'key_added' to rank_genes_groups 15 May 2018, 12:23:04 UTC
9a754bb falexwolf 15 May 2018, 10:47:57 UTC fixed export_to_gexf 15 May 2018, 10:47:57 UTC
e9ae4ff Alex Wolf 14 May 2018, 08:45:33 UTC Merge pull request #152 from gokceneraslan/gzbz2 Allow gz and bz2 extensions for text formats 14 May 2018, 08:45:33 UTC
b0093d1 falexwolf 13 May 2018, 23:19:51 UTC added function for graph comparisons 13 May 2018, 23:19:51 UTC
68170a0 falexwolf 13 May 2018, 22:18:54 UTC treat disconnected graphs in DPT properly 13 May 2018, 22:18:54 UTC
1247336 Gökcen Eraslan 13 May 2018, 10:46:34 UTC Strip lines in soft.gz 13 May 2018, 10:46:34 UTC
3900f72 Gökcen Eraslan 13 May 2018, 10:42:04 UTC Fix for soft.gz 13 May 2018, 10:42:04 UTC
7db64ad Gökcen Eraslan 13 May 2018, 10:32:24 UTC Write gz/bz2 support to error message too 13 May 2018, 10:32:24 UTC
cad3ecb Gökcen Eraslan 13 May 2018, 10:26:56 UTC txt.gz is also supported 13 May 2018, 10:26:56 UTC
6e789a6 Gökcen Eraslan 13 May 2018, 10:19:37 UTC Allow gz and bz2 extensions for text formats 13 May 2018, 10:19:37 UTC
c1eb149 falexwolf 13 May 2018, 04:34:50 UTC pca can now again process arrays and sparse matrices 13 May 2018, 04:34:50 UTC
aa999d5 falexwolf 12 May 2018, 00:16:08 UTC allow pl.paga with umap and edges 12 May 2018, 00:16:08 UTC
b12d5e2 falexwolf 11 May 2018, 21:59:38 UTC used shape attribute of adata in DPT 11 May 2018, 21:59:38 UTC
0da2f4a falexwolf 11 May 2018, 20:05:22 UTC allow arbitrarily named basis in scatter 11 May 2018, 20:05:28 UTC
1febb64 Alex Wolf 11 May 2018, 15:20:07 UTC Merge pull request #151 from Koncopd/master Use chunked_X 11 May 2018, 15:20:07 UTC
bb94c91 Sergei Rybakov 11 May 2018, 15:05:44 UTC Merge branch 'chunks' 11 May 2018, 15:05:44 UTC
38ea134 Sergei Rybakov 08 May 2018, 18:09:06 UTC chunks_X -> chunked_X 08 May 2018, 18:09:06 UTC
6287fc0 Sergei Rybakov 08 May 2018, 17:47:54 UTC changed pca - removed recursion, process only AnnData objects 08 May 2018, 17:47:54 UTC
617754b falexwolf 07 May 2018, 23:04:27 UTC fixed little bug in init_pos=paga 07 May 2018, 23:04:27 UTC
13231a3 falexwolf 07 May 2018, 21:40:10 UTC updated docs of DPT 07 May 2018, 21:40:10 UTC
161edd7 falexwolf 07 May 2018, 20:37:46 UTC allow exporting label positions on plots 07 May 2018, 20:37:46 UTC
dd472e3 falexwolf 07 May 2018, 15:08:58 UTC option for plotting without legend 07 May 2018, 15:08:58 UTC
53ee0e8 falexwolf 07 May 2018, 14:55:03 UTC set random seed when initializing with paga 07 May 2018, 14:55:03 UTC
259c80b falexwolf 07 May 2018, 14:44:46 UTC added note about default min_dist in UMAP 07 May 2018, 14:44:46 UTC
f224349 falexwolf 07 May 2018, 14:28:50 UTC add convenience for saving with transparent background 07 May 2018, 14:28:50 UTC
1835100 falexwolf 07 May 2018, 02:01:21 UTC improved paga visualization and benchmarking 07 May 2018, 02:01:30 UTC
36b521b falexwolf 07 May 2018, 02:01:05 UTC use copy in neighbors to prevent bug 07 May 2018, 02:01:30 UTC
530b6bd falexwolf 06 May 2018, 23:56:11 UTC speedup in exporting module 07 May 2018, 02:01:30 UTC
6473449 Sergei Rybakov 06 May 2018, 20:59:48 UTC chunks 06 May 2018, 20:59:48 UTC
57e910c Alex Wolf 06 May 2018, 18:47:55 UTC Merge pull request #149 from gokceneraslan/patch-6 Fix UMAP metric_kwds parameter 06 May 2018, 18:47:55 UTC
58d6d8b Gökçen Eraslan 06 May 2018, 17:11:07 UTC Fix UMAP metric_kwds parameter 06 May 2018, 17:11:07 UTC
acd85c7 falexwolf 06 May 2018, 02:28:37 UTC cleaned up paga 06 May 2018, 02:28:37 UTC
e859035 falexwolf 06 May 2018, 01:05:51 UTC updated SPRING export 06 May 2018, 01:06:35 UTC
fe6232a Alex Wolf 05 May 2018, 01:36:49 UTC Merge pull request #147 from fbrundu/patch-1 Fixed Pandas .loc notation and added gene_names parameter to violin 05 May 2018, 01:36:49 UTC
3509fdd falexwolf 05 May 2018, 01:15:39 UTC major clean up 05 May 2018, 01:15:39 UTC
2f63cdc Francesco G. Brundu 04 May 2018, 22:38:12 UTC Fixed Pandas .loc notation and added gene_names parameter to violin 04 May 2018, 22:38:12 UTC
6c46667 falexwolf 04 May 2018, 22:07:16 UTC reorganized settings 04 May 2018, 22:07:16 UTC
4a053f9 falexwolf 04 May 2018, 21:32:38 UTC fall back to fr layout when fa2 is not installed 04 May 2018, 21:32:38 UTC
3500e01 falexwolf 04 May 2018, 21:27:39 UTC better organization of default figure configuration and docs 04 May 2018, 21:27:39 UTC
639dcd4 Alex Wolf 03 May 2018, 14:46:03 UTC Merge pull request #139 from scottgigante/master Add PHATE to API docs 03 May 2018, 14:46:03 UTC
287a494 Scott Gigante 03 May 2018, 13:38:30 UTC add PHATE to API docs 03 May 2018, 13:38:30 UTC
b9c882c falexwolf 03 May 2018, 10:59:17 UTC cleaned up phate 03 May 2018, 10:59:17 UTC
8d92dd3 Alex Wolf 03 May 2018, 10:51:20 UTC Merge pull request #136 from scottgigante/master Add PHATE integration 03 May 2018, 10:51:20 UTC
c542584 falexwolf 03 May 2018, 00:03:52 UTC support pngs within vector graphics 03 May 2018, 00:03:52 UTC
c3555c4 Scott Gigante 02 May 2018, 18:40:28 UTC fix typo 02 May 2018, 18:40:28 UTC
e246af7 Scott Gigante 02 May 2018, 18:27:12 UTC add github to PHATE docstring 02 May 2018, 18:27:12 UTC
1ceccc0 Scott Gigante 02 May 2018, 18:23:41 UTC make PHATE and TSNE APIs match 02 May 2018, 18:23:41 UTC
d6759b0 falexwolf 02 May 2018, 16:09:26 UTC added working velocyto-paga combination 02 May 2018, 16:09:26 UTC
c42e4d2 falexwolf 02 May 2018, 03:22:27 UTC return single axis if plotting single key 02 May 2018, 03:22:27 UTC
f70862a Scott Gigante 01 May 2018, 16:03:46 UTC remove temporary raise 01 May 2018, 16:03:46 UTC
12ed545 Scott Gigante 01 May 2018, 16:00:57 UTC add test, avoid namespace issues 01 May 2018, 16:00:57 UTC
aa8b286 Scott Gigante 01 May 2018, 15:36:35 UTC add PHATE integration 01 May 2018, 15:36:35 UTC
4edb0b5 falexwolf 01 May 2018, 00:17:09 UTC added docs for forceatlas2 and changed acronym 01 May 2018, 00:17:09 UTC
d043e59 falexwolf 01 May 2018, 00:08:10 UTC prettfied pypairs and added to docs 01 May 2018, 00:08:10 UTC
107863c falexwolf 30 April 2018, 23:57:32 UTC cleaned up addition of mnn_correct 30 April 2018, 23:57:32 UTC
414e7e3 Alex Wolf 30 April 2018, 23:34:03 UTC Merge pull request #131 from chriscainx/master Added wrapper for mnnpy 30 April 2018, 23:34:03 UTC
3f29b54 Alex Wolf 30 April 2018, 23:32:06 UTC Merge pull request #134 from gokceneraslan/patch-5 Exclude nans from normalized dispersion vector 30 April 2018, 23:32:06 UTC
7469076 falexwolf 30 April 2018, 10:43:51 UTC respect number of pcs even for fallback 30 April 2018, 10:43:51 UTC
8ac4bce Gökçen Eraslan 27 April 2018, 09:25:18 UTC Exclude nans from normalized dispersion vector `nan`s accumulate in the beginning of `dispersion_norm` vector and lead to an overestimated dispersion cutoff, if there are zero-expression genes. Fixes #115. 27 April 2018, 09:25:18 UTC
e1df057 falexwolf 26 April 2018, 05:54:06 UTC added a threshold parameter to pl.paga 26 April 2018, 17:21:58 UTC
150d44c Alex Wolf 26 April 2018, 16:37:21 UTC Merge pull request #133 from dawe/master fixes #105 and addresses some issues when nan are introduced 26 April 2018, 16:37:21 UTC
9a23049 dawe 26 April 2018, 10:35:08 UTC fixes #105 and addresses some issues when nan are introduced 26 April 2018, 10:35:08 UTC
e235c58 Chris Kang 26 April 2018, 09:38:55 UTC added wrapper for mnnpy 26 April 2018, 09:38:55 UTC
54f6ba1 falexwolf 26 April 2018, 01:10:20 UTC added forceatlas2 layout to draw_graph 26 April 2018, 01:10:20 UTC
12f9caa falexwolf 25 April 2018, 14:43:21 UTC fixed bug in reexport 25 April 2018, 14:43:21 UTC
190379f falexwolf 25 April 2018, 14:36:45 UTC prettified pypairs 25 April 2018, 14:36:45 UTC
1ac482c falexwolf 25 April 2018, 01:16:41 UTC added reexport for mnn_concatenate 25 April 2018, 01:16:41 UTC
9a8bb7a falexwolf 25 April 2018, 00:50:27 UTC moved mnn_concatenate to rtools 25 April 2018, 00:50:27 UTC
eeeea26 falexwolf 25 April 2018, 00:42:17 UTC removed the just introduced rpy2 from requirements 25 April 2018, 00:42:17 UTC
c7c2738 Alex Wolf 25 April 2018, 00:41:18 UTC Merge pull request #125 from chriscainx/master Added MNN_correct support 25 April 2018, 00:41:18 UTC
94737cf Alex Wolf 25 April 2018, 00:33:32 UTC Merge pull request #130 from theislab/rna_velocity rna velocity 25 April 2018, 00:33:32 UTC
6793d4d falexwolf 23 April 2018, 21:56:25 UTC summarized notebook state in velocity module 23 April 2018, 21:56:25 UTC
7aaf766 falexwolf 23 April 2018, 21:00:37 UTC clean up rna velocity trials 23 April 2018, 21:00:37 UTC
9caf460 falexwolf 20 April 2018, 18:12:23 UTC further towards RNA velocity 20 April 2018, 18:12:23 UTC
fdf522d falexwolf 19 April 2018, 09:22:44 UTC further steps towards rna velocity 19 April 2018, 09:32:28 UTC
c9c63bf falexwolf 18 April 2018, 22:36:30 UTC drafted rna velocity for paga 19 April 2018, 09:32:28 UTC
32afcfd falexwolf 18 April 2018, 19:57:27 UTC raise error when calling normalize_per_cell with array and copy=False 19 April 2018, 09:32:28 UTC
9913591 falexwolf 18 April 2018, 11:50:27 UTC draft or rna_velocity 19 April 2018, 09:32:28 UTC
c241098 falexwolf 19 April 2018, 09:31:10 UTC introduced gene_symbols parameter in rank_genes_groups 19 April 2018, 09:31:10 UTC
06bb569 falexwolf 18 April 2018, 11:53:10 UTC local import of pypairs and check whether it's installed 18 April 2018, 11:53:10 UTC
c405363 Alex Wolf 18 April 2018, 11:49:30 UTC Merge pull request #126 from rfechtner/include-pypairs Include pypairs 18 April 2018, 11:49:30 UTC
4f68892 rfechtner 18 April 2018, 11:39:34 UTC Update tl.py 18 April 2018, 11:39:34 UTC
3efd51c rfechtner 18 April 2018, 11:39:13 UTC removed dataset dependant method 18 April 2018, 11:39:13 UTC
bfbc784 falexwolf 18 April 2018, 09:45:34 UTC use dense distance matrix when knn is False 18 April 2018, 09:45:34 UTC
394ccda falexwolf 18 April 2018, 09:42:35 UTC properly exploit categorical data in regress_out 18 April 2018, 09:42:43 UTC
1024a70 rfechtner 18 April 2018, 09:41:01 UTC added pypairs 18 April 2018, 09:41:01 UTC
1f45978 rfechtner 18 April 2018, 09:40:22 UTC included pypairs tools 18 April 2018, 09:40:22 UTC
ac39b21 falexwolf 18 April 2018, 09:31:17 UTC added sanitize anndata for regress out 18 April 2018, 09:31:17 UTC
3000d37 Chris Kang 17 April 2018, 12:20:37 UTC fixed requirements 17 April 2018, 12:20:37 UTC
bb808b6 Chris Kang 17 April 2018, 12:15:28 UTC fixed a small thing with rpy2 interface 17 April 2018, 12:15:28 UTC
bce65f8 Chris Kang 17 April 2018, 12:01:12 UTC fixed type 17 April 2018, 12:01:12 UTC
2d30edf Chris Kang 17 April 2018, 11:58:04 UTC Added wrapper for mnnCorrect from scran 17 April 2018, 11:58:04 UTC
bdc26cf falexwolf 16 April 2018, 20:51:47 UTC raise error when using an invalid category for reclustering 16 April 2018, 20:51:47 UTC
705b64a falexwolf 16 April 2018, 20:27:40 UTC updated setup to contain versioneer cmdclass and display proper version numbers again 16 April 2018, 20:27:40 UTC
6ba0615 falexwolf 16 April 2018, 17:44:48 UTC set _sdist to versioneer 16 April 2018, 17:44:48 UTC
5679f7b falexwolf 16 April 2018, 16:39:57 UTC added statsmodels to conda install 16 April 2018, 16:40:10 UTC
f6726f0 Alex Wolf 16 April 2018, 15:43:13 UTC Merge pull request #124 from gokceneraslan/patch-4 Do not use paga in draw_graph, if use_paga is False 16 April 2018, 15:43:13 UTC
3160697 Gökçen Eraslan 16 April 2018, 15:20:33 UTC Do not use paga is use_paga is False This fixes the exception that happens in following scenario: sc.tl.louvain(adata) sc.tl.paga(adata) sc.pl.paga(adata) sc.tl.draw_graph(adata) Since there is no else statement for use_paga check, ig_layout is not defined. 16 April 2018, 15:20:33 UTC
33bccc7 falexwolf 11 April 2018, 08:51:00 UTC clarified UMAP docs 11 April 2018, 08:56:47 UTC
back to top