Cancer Systems Immunology Lab

ProjecTILs

Interpretation of cell states using reference single-cell maps

UCell

Gene set scoring for single-cell data

scGate

marker-based purification of cell types from single-cell RNA-seq datasets

STACAS

R package for semi-supervised single-cell data integration

SignatuR

A database of useful gene signatures for single-cell analysis

ProjecTILs_CaseStudies

A repository of case studies using ProjecTILs

TILPRED

Tumor-Infiltrating CD8 Lymphocytes states prediction

GeneNMF

Methods to perform NMF on single-cell data

HiTME

High-resolution Tumor Micro-Environment cell type classification and compositional analysis for scRNA-seq

scGate.demo

scGate_models

Cell type gating models for scGate

scIntegrationMetrics

R implementation of integration metrics for single-cell data

CD8_human_TIL_atlas_construction

human_CD8_TIL_CaseStudies

Projection example using a human CD8 TIL reference map.

LiTang_IL10_CART

Tcell_clonal_analysis

Reproducible code for reference-based T cell clonal analysis

UCell_demo

ProjecTILs.demo

A repository for testing the functionalities of ProjecTILs

.github

Course_scRNA-seq_Exercise1

This is the first exercise for the bioinformatics scRNA-seq course

DC_atlas

GEEP_Jesus_Nov2021

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.

scRepertoire

A toolkit for single-cell immune profiling

seurat-wrappers

Community-provided extensions to Seurat

STACAS.demo

Integrating scRNA-seq data using STACAS

TCRanker