chanzuckerberg cellxgene-census issues

chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census

https://chanzuckerberg.github.io/cellxgene-census/

MIT License

72 stars 19 forks source link

issues

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[python] Geneformer CLS embeddings

#1225 mlin opened 15 hours ago
1
[python] dataloader optimization (picking up 1169)

#1224 ivirshup opened 3 days ago
1
[ci] Test GH concurrency

#1223 ebezzi opened 3 days ago
1
Add live Census tests for PyTorch loaders

#1222 ebezzi opened 3 days ago
0
[python] Fix ExperimentDataPipe length

#1221 ebezzi opened 4 days ago
1
update metrics

#1220 pablo-gar opened 4 days ago
1
[pytorch] Add encoders for X

#1219 ebezzi opened 5 days ago
0
pip install problems

#1218 Sankar-Gollapudi opened 6 days ago
8
Bulk download h5ad data with filters [R]

#1217 myushen opened 6 days ago
1
What is the difference between tissue and tissue_general

#1216 Alex2975 closed 5 days ago
5
[python] Stop including `"do_not_delete"` key in result of `get_census_version_directory`

#1215 ivirshup closed 4 days ago
1
[docs] Add PyTorch loaders article release

#1214 pablo-gar opened 1 week ago
1
[python] Require scikit-misc < 0.4

#1213 ebezzi closed 1 week ago
1
[docs] Update citation notebook

#1212 pablo-gar closed 1 week ago
0
[docs] Update schema doc for version 2.1.0

#1211 ebezzi closed 1 week ago
1
[docs] Update census data release page with upcoming LTS information

#1210 pablo-gar opened 1 week ago
0
[docs] Update census data release page with upcoming LTS information

#1209 pablo-gar closed 1 week ago
0
[python] Fix typo in embedding notebook

#1208 ivirshup closed 1 week ago
0
[python] Check census version for get_all_available_embeddings

#1207 ivirshup closed 1 week ago
1
Embeddings notebook typo leads to saving scvi embedding to `adata.obsm["geneformer"]`

#1206 ivirshup closed 1 week ago
0
embeddings functions do not support same values for `organisms` as main API

#1205 ivirshup opened 1 week ago
0
get_census_version_directory() has `do_not_delete` key, which isn't documented or in the type definitions

#1204 ivirshup closed 4 days ago
1
[Docs] Adds missing changelog for `cellxgene_census_schema.md`

#1203 pablo-gar closed 1 week ago
0
Validate census version for embeddings

#1202 ivirshup closed 1 week ago
1
How to download and use local soma directory from cellxgene_census.open_soma()?

#1201 Alex2975 closed 1 week ago
7
[builder] Add collection_doi_label to the datasets dataframe

#1200 ebezzi closed 1 week ago
1
GeneformerTokenizer updates

#1199 mlin closed 2 days ago
1
Missing column in docs for cellxgene_census schema

#1198 emdann closed 1 week ago
1
[python] fix mypy complaint in experimental/_embedding.py

#1197 mlin closed 2 weeks ago
2
[python] CensusSCVIDataModule + notebook

#1196 ebezzi opened 2 weeks ago
4
Can we use soma_joinid as cell_id

#1195 Alex2975 closed 2 weeks ago
4
Census Builder should ingest to CXG schema 5.1.0 datasets

#1194 prathapsridharan opened 3 weeks ago
1
[python] set user-agent

#1193 ivirshup closed 4 days ago
2
[builder] Upgrade to CELLxGENE schema 5.1

#1192 Bento007 closed 1 week ago
2
[python] Support custom obs encoders

#1191 ebezzi closed 1 day ago
1
[python] Remove pytorch pin

#1190 ebezzi closed 2 weeks ago
1
[python] Follow spec-0

#1189 ivirshup opened 1 month ago
4
[pytorch] Set shuffle as default in pytorch, use new algorithm

#1188 ebezzi closed 1 month ago
1
[python] Relax pin: `tiledbsoma~=1.11.4`

#1187 ryan-williams closed 1 month ago
2
Fix incorrect logger calls

#1186 prathapsridharan closed 1 month ago
1
Prepare for 1.14.1 release

#1185 ebezzi closed 1 month ago
1
[python] Restore soma indexer in hvg

#1184 ebezzi closed 1 month ago
3
Unexpected behavior when getting length of ExperimentDatapipe

#1183 jdenhof opened 1 month ago
3
ExperimentDataPipe should record the iterated joinids

#1182 ebezzi opened 1 month ago
0
Do not hardcode bucket names in the Census codebase

#1181 ebezzi opened 1 month ago
0
Implement `collection_doi_label` in builder

#1180 pablo-gar closed 1 week ago
0
Draft schema for `collection_doi_label` of `census["census_info"]["dataset"]`

#1179 pablo-gar opened 1 month ago
3
[python] Fix wrong parameters in ExperimentDataPipe

#1178 ebezzi closed 1 month ago
2
Follow SPEC-0 for minimum supported versions of dependencies

#1177 ivirshup opened 1 month ago
0
[docs] Add notebook symlink 2

#1176 ebezzi closed 1 month ago
1