chanzuckerberg/cellxgene-census

Issues

• Census LTS update

  #1303 opened 3 months ago by cathystoli
  1

• Provide field descriptors study-level metadata outside of cellxgene schema

  #1321 opened 20 days ago by emdann
  6

• Current stable data release has fewer cancer cells than "2023-05-15"

  #1255 opened a month ago by YubinXie
  11

• problems in installation

  #1316 opened 2 months ago by inestm28
  2

• differential expression - memento

  #1282 opened 4 months ago by MatthiasBeyens
  2

• Stop linking release cycles of R and Python packages

  #1293 opened 2 months ago by ivirshup
  0

• Running the geneformer example results in KeyError

  #1312 opened 2 months ago by ddemaeyer
  1

• DoesNotExistError: 's3://cellxgene-census-public-us-west-2/cell-census/2023-12-15/soma/' does not exist

  #1313 opened 2 months ago by yabeykoon
  3

• Which columns should be included in var?

  #1301 opened 2 months ago by ivirshup
  4

• Cellxgene Data Discrepancy between cellxgene website and cellxgene_census

  #1311 opened 2 months ago by Feilijiang
  2

• CI jobs sometimes die because Karpenter wants to move jobs

  #1307 opened 2 months ago by ivirshup
  1

• NMF census model appears to not be available on the R side

  #1299 opened 2 months ago by hlmtran
  2

• Add approved assays to accepted assay list

  #1302 opened 2 months ago by jahilton
  7

• feature_dataset_presence_matrix should include genes with 0 counts

  #1284 opened 4 months ago by ebezzi
  3

• Specify the Census search space with an `obs_value_filter` parameter in `find_nearest_obs`

  #1305 opened 2 months ago by pablo-gar
  1

• CI jobs sometimes die because Karpenter wants to move jobs

  #1306 opened 2 months ago by ivirshup
  0

• [R] cellxgene-census `PermanentRedirect` S3 error

  #1261 opened 5 months ago by JHYSiu
  17

• Social previews for the docsite

  #1295 opened 3 months ago by ivirshup
  0

• Fix docs for data loaders

  #1291 opened 3 months ago by ivirshup
  1

• Experiment Data Pipe doesn't return soma_joinids

  #1289 opened 3 months ago by yanwu2014
  2

• Stop blocking Boroni collection

  #1263 opened 5 months ago by ivirshup
  0

• Python CI process killed with tiledbsoma 1.14.1

  #1288 opened 3 months ago by ivirshup
  1

• Identical values reported for "var.nnz" and "var.n_measured_obs" for different datasets retrieved via get_anndata()

  #1281 opened 4 months ago by khughitt
  1

• Bug with get_all_available_embeddings

  #1283 opened 3 months ago by huguesva
  6

• open_soma error: The bucket you are attempting to access must be addressed using the specified endpoint.

  #1285 opened 3 months ago by ybukhman
  2

• Adding a dataset of `tissue_type = "organoid"` to Census scVI embedding

  #1271 opened 4 months ago by kavithakrishna1
  0

• [R] Remove tiledb dependency for R package

  #1274 opened 4 months ago by ivirshup
  1

• Stop auto-closing issues

  #1268 opened 4 months ago by ivirshup
  1

• Add live Census tests for PyTorch loaders

  #1222 opened 6 months ago by ebezzi
  0

• [pytorch] Add encoders for X

  #1219 opened 6 months ago by ebezzi
  1

• Add function for listing available h5ads for download

  #1251 opened 5 months ago by ivirshup
  3

• Network Issue FAQs

  #1265 opened 5 months ago by cathystoli
  1

• Bump tiledbsoma version on builder to 1.12.3

  #1243 opened 6 months ago by ivirshup
  11

• ConnectionResetError(104, 'Connection reset by peer') when using cellxgene_census.get_anndata

  #1260 opened 5 months ago by xshaaaa
  7

• embeddings functions do not support same values for `organisms` as main API

  #1205 opened 6 months ago by ivirshup
  0

• tools/census_contrib/pyproject.toml is super out of date

  #1254 opened 5 months ago by ivirshup
  0

• TimeoutError with cellxgene_census.get_anndata()

  #1253 opened 5 months ago by LysSanzMoreta
  7

• cellxgene-census times out running through a proxy server

  #1256 opened 5 months ago by kgweiss
  5

• [misc] user-agent tagging in R

  #1249 opened 6 months ago by pablo-gar
  0

• Bulk download h5ad data with filters [R]

  #1217 opened 6 months ago by myushen
  1

• Execution Time for highly_variable_genes Function

  #1242 opened 6 months ago by ckrilow
  2

• Support numpy 2

  #1240 opened 6 months ago by ivirshup
  0

• pip install problems

  #1218 opened 6 months ago by Sankar-Gollapudi
  9

• What is the difference between tissue and tissue_general

  #1216 opened 6 months ago by Alex2975
  5

• get_census_version_directory() has `do_not_delete` key, which isn't documented or in the type definitions

  #1204 opened 6 months ago by ivirshup
  1

• Validate census version for embeddings

  #1202 opened 6 months ago by ivirshup
  1

• Embeddings notebook typo leads to saving scvi embedding to `adata.obsm["geneformer"]`

  #1206 opened 6 months ago by ivirshup
  0

• How to download and use local soma directory from cellxgene_census.open_soma()?

  #1201 opened 6 months ago by Alex2975
  7

• Missing column in docs for cellxgene_census schema

  #1198 opened 6 months ago by emdann
  1

• Can we use soma_joinid as cell_id

  #1195 opened 7 months ago by Alex2975
  4