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Published June 5, 2025 | Version 2025-06-05
Software Open

AlexsLemonade/OpenScPCA-analysis: 2025-06-05

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 shell script to run SCPCP000015 by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1115
  • Add ewings infercnv template notebook by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1118
  • Add ewings palette file by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1123
  • Template notebook fix by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1124
  • Add celltype reference file by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1128
  • Add script to run inferCNV with an "internal" reference by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1126
  • Notebook text patch by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1131
  • Don't include PDX samples in the normal references by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1135
  • Add brief exploratory notebook for normal references by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1140
  • Notebook to directly compared pooled vs internal references for ewings by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1144
  • Add brief ewings conclusions to README by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1150
  • Use docker in infercnv-consensus-cell-type by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1158

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

Files

AlexsLemonade/OpenScPCA-analysis-2025-06-05.zip

Files (1.3 GB)

Additional details

Related works

Is supplement to
Software: https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/2025-06-05 (URL)

Software

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