Cancer Systems Immunology Lab's repositories
ProjecTILs
Interpretation of cell states using reference single-cell maps
ProjecTILs_CaseStudies
A repository of case studies using ProjecTILs
scGate_models
Cell type gating models for scGate
scIntegrationMetrics
R implementation of integration metrics for single-cell data
human_CD8_TIL_CaseStudies
Projection example using a human CD8 TIL reference map.
Tcell_clonal_analysis
Reproducible code for reference-based T cell clonal analysis
Yerly_BCC_wounding
Code to reproduce the results by Yerly et al. (2024)
Course_scRNA-seq_Exercise1
This is the first exercise for the bioinformatics scRNA-seq course
ProjecTILs.demo
A repository for testing the functionalities of ProjecTILs
GeneNMF.demo
Demos and applications for NMF on single-cell data
HiTME_CaseStudies
Repository of case studies using HiTME
scib-pipeline
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
scib-pipeline-2
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
seurat-wrappers
Community-provided extensions to Seurat
STACAS.demo
Integrating scRNA-seq data using STACAS