Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"

Single-cell analysis in Python. Scales to >1M cells.

Multi-subject Single Cell Deconvolution

The Mojo Programming Language

A list of deep learning implementations in biology

mitochondrial variant analysis tools

tools for analysing Biscuit (https://github.com/zwdzwd/biscuit/wiki/Align-bisulfite-converted-reads) output

BISuilfite-seq CUI Toolkit

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cell type deconvolution for multi-condition bulk RNA-seq data

RNA-seq workflow using STAR and DESeq2

Gene regulatory network inference using fused LASSO on multiple data sets: application to Escherichia coli