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carmonalab.github.io

cd8_human_til_atlas_construction

course_scrna-seq_exercise1

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

dc_atlas

geep_jesus_nov2021

genenmf

Methods to perform NMF on single-cell data

genenmf.demo

Demos and applications for NMF on single-cell data

hitme

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

hitme_casestudies

Repository of case studies using HiTME

human_cd8_til_casestudies

Projection example using a human CD8 TIL reference map.

isee_shiny_cd8til_2019

litang_il10_cart

projectils

Interpretation of cell states using reference single-cell maps

projectils.demo

A repository for testing the functionalities of ProjecTILs

projectils_casestudies

A repository of case studies using ProjecTILs

scgate

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

scgate.benchmark

scgate.demo

scgate_models

Cell type gating models for scGate

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.

scintegrationmetrics

R implementation of integration metrics for single-cell data

screpertoire

A toolkit for single-cell immune profiling

seurat-wrappers

Community-provided extensions to Seurat

shiny

This version of rocker/shiny has additional packages to enable iSEE Explorer support

signatur

A database of useful gene signatures for single-cell analysis

stacas

R package for semi-supervised single-cell data integration

stacas.demo

Integrating scRNA-seq data using STACAS

tcell_clonal_analysis

Reproducible code for reference-based T cell clonal analysis