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Published August 20, 2025 | Version 2025-08-20
Software Open

AlexsLemonade/OpenScPCA-analysis: 2025-08-20

Authors/Creators

  • 1. @AlexsLemonade
  • 2. Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation
  • 3. St. Anna Children's Cancer Research Institute (CCRI)
  • 4. Alex's Lemonade Stand Foundation
  • 5. UT Southwestern
  • 6. MD Anderson Cancer Center
  • 7. UCL

Description

What's Changed

  • Add reference cell group table by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1162
  • Add neuroblastoma CNVs to reference tsv by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1159
  • Exploratory notebook of NB normal reference options by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1161
  • Initiate NB analysis module by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1170
  • Reformat NBAtlas to SCE and AnnData objects by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1173
  • Add marker genes for NB cell type validation by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1181
  • Script to train SingleR model with NBAtlas by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1187
  • Add script to run SingleR by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1192
  • Add optparse to ETP module by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1203
  • Exploratory notebook comparing aggregated & non-aggregated by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1194
  • NB module: Docker and remove cell id script by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1205
  • Perform exploration of splitting NE cells by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1206
  • Reorganize and lay groundwork for testing gene filtering by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1208
  • Patch fix - model file name by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1209
  • Explore gene filtering NBAtlas before SingleR by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1210
  • Update code using cell-type-consensus results by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1198
  • Update which NBAtlas label we use by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1218
  • Update marker gene TSVs by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1222
  • Notebook for all singler results by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1211
  • Spelling and anndata conversion by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1225
  • Analysis module creation for Osteosarcoma celltype analysis by @rs25-code in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1224
  • Update NBAtlas anndata reference preparation by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1230
  • Update conda lock for Ewings by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1233
  • Script to prepare anndata query object by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1231
  • SingleR report: library size and PDX by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1236
  • Try to fix Ewing error by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1237
  • Add git into (non)-ETP docker by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1240
  • Add script to generate NB normal references by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1169
  • Patch the (non)-ETP-ALL modules by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1238
  • Update environment to use scANVI in CPU by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1243
  • Add scANVI training script by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1247
  • Patch for CI for wilms-06 module by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1258
  • Update sample count in docs by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1260
  • Initiate module for annotating samples with SCimilarity by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1265
  • Add scANVI query script by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1248
  • Add reference TSV file with cell type annotations and ontology IDs for SCimilarity labels by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1268
  • Add conda environment for SCimilarity by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1274
  • Add scANVI exploratory notebook by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1269
  • Add NBAtlas ontology ids by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1277
  • Remove the myeloid grouping and update accordingly by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1279
  • Final.final NB annotation notebook by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1282

New Contributors

  • @rs25-code made their first contribution in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1224

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2025-06-05...2025-08-20

Files

AlexsLemonade/OpenScPCA-analysis-2025-08-20.zip

Files (1.4 GB)

Additional details

Related works

Is supplement to
Software: https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/2025-08-20 (URL)

Software

Repository URL
https://github.com/AlexsLemonade/OpenScPCA-analysis