AlexsLemonade/OpenScPCA-analysis

View on GitHub

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal

Stars: 16
Forks: 24
Open beginner issues: 0
Indexed issues: 42
Avg merge: 3d 23h
Merged PRs (30d): 3

Dominant language: HTML
License: No license data
Last GitHub push: Sep 11, 2026
Latest indexed: Sep 14, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Open All

42 open issues indexed

Doc: Ways to contribute Open

documentation

AlexsLemonade/OpenScPCA-analysis#147 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[Optional] Doc: What happens after you file a PR? Open

documentation

AlexsLemonade/OpenScPCA-analysis#210 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Expand troubleshooting documentation Open

documentation

AlexsLemonade/OpenScPCA-analysis#299 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Consider adding option to the data download script to list files Open

OpenScPCA admin

AlexsLemonade/OpenScPCA-analysis#414 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Docs request: Reframe the "running an analysis module" doc Open

documentation

AlexsLemonade/OpenScPCA-analysis#475 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Docs request: Organizing your module results Open

documentation

AlexsLemonade/OpenScPCA-analysis#502 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Exploratory analysis notebook for SEACells Open

analysis

AlexsLemonade/OpenScPCA-analysis#611 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Additional docs for troubleshooting precommit Open

documentation

AlexsLemonade/OpenScPCA-analysis#645 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Future idea: Use SingleR with SCPCL000822 and SCPCL000824 as references to annotate remaining Ewing samples Open

analysis

AlexsLemonade/OpenScPCA-analysis#668 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Cell Type Annotation of Osteosarcoma snRNA-seq Data (SCPCP000017) Open

analysis

AlexsLemonade/OpenScPCA-analysis#687 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
DSRCT Dataset Analysis (SCPCP000013) #583 Open

analysis

AlexsLemonade/OpenScPCA-analysis#701 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Celltype annotation for non-ETP ALL (SCPCP000003) Open

analysis

AlexsLemonade/OpenScPCA-analysis#761 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Initiation of SCPCP000001 Open

analysis

AlexsLemonade/OpenScPCA-analysis#778 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
celltype/tumor annotation for non-ETP T-ALL (SCPCP000003) Open

analysis

AlexsLemonade/OpenScPCA-analysis#787 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Keep tabs on Rhtslib installation in Dockerfiles Open

OpenScPCA admin

AlexsLemonade/OpenScPCA-analysis#803 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Attempt to identify tumor cells in those non-ETP samples without B cells (SCPCP000003) Open

analysis

AlexsLemonade/OpenScPCA-analysis#811 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
cell type/tumor annotation for ETP T-ALL (SCPCP000003) Open

analysis

AlexsLemonade/OpenScPCA-analysis#822 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Docs request: FAQ about gene id conversion Open

AlexsLemonade/OpenScPCA-analysis#837 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Modify/explore clustering for Wilms tumor annotation (SCPCP000014) Open

analysis

AlexsLemonade/OpenScPCA-analysis#840 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Improve Wilms Tumor Dataset Annotation (SCPCP000006) - explore `predicted.score` and `has_cnv.score` thresholds Open

analysis

AlexsLemonade/OpenScPCA-analysis#856 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Integration of the SCPCP000006 Wilms tumor dataset Open

analysis

AlexsLemonade/OpenScPCA-analysis#857 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Decrease size of docker image for Ewing's module Open

AlexsLemonade/OpenScPCA-analysis#884 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Notebook to explore using normal cell references to annotate tumor cell states in Ewing sarcoma samples Open

analysis

AlexsLemonade/OpenScPCA-analysis#941 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Docs request: "Quick start" guide for technical setup Open

AlexsLemonade/OpenScPCA-analysis#948 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Consider using a converted Seurat object in hello-clusters Open

AlexsLemonade/OpenScPCA-analysis#957 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Bug report: Zellkonverter/Basilisk initialization in Docker images doesn't work with rstudio users Open

bug

AlexsLemonade/OpenScPCA-analysis#972 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Explore cells that are classified as both immune and tumor in Ewing samples Open

analysis

AlexsLemonade/OpenScPCA-analysis#1087 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Docs request: Centralized documentation for available results Open

OpenScPCA admin

AlexsLemonade/OpenScPCA-analysis#1119 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Pilocytic Astrocytoma scRNA Analysis Open

analysis

AlexsLemonade/OpenScPCA-analysis#1121 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add wrapper function for running internal references Open

analysis

AlexsLemonade/OpenScPCA-analysis#1130 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Explore use of pooled normal reference with inferCNV in solid tumors of interest Open

Epic

AlexsLemonade/OpenScPCA-analysis#1143 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Run inferCNV on neuroblastoma samples Open

analysis

AlexsLemonade/OpenScPCA-analysis#1148 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use CNV distributions to identify additional Ewings tumor cells Open

AlexsLemonade/OpenScPCA-analysis#1156 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add function to create total CNV column Open

analysis

AlexsLemonade/OpenScPCA-analysis#1157 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Osteosarcoma SCPCAB0027 - Tumor versus Normal cell differentiation and annotation Open

analysis

AlexsLemonade/OpenScPCA-analysis#1193 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Record project-specific normal reference groups in TSVs Open

AlexsLemonade/OpenScPCA-analysis#1239 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Don't recommend use of osx-64 platform for conda-lock Open

AlexsLemonade/OpenScPCA-analysis#1244 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update immune cell types file in `cell-type-consensus` Open

AlexsLemonade/OpenScPCA-analysis#1391 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Add script to prepare references for use Open

analysis

AlexsLemonade/OpenScPCA-analysis#1413 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Add script to train SingleR model Open

analysis

AlexsLemonade/OpenScPCA-analysis#1414 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Evaluate reference approach for annotating osteosarcoma samples Open

analysis

AlexsLemonade/OpenScPCA-analysis#1424 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Create preliminary plots evaluating metaprograms from Neuroblastoma pilot Open

analysis

AlexsLemonade/OpenScPCA-analysis#1431 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

AlexsLemonade/OpenScPCA-analysis

Get new issues in your inbox