oncologylab/craftgrn

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

Research code accompanying AlphaGenome

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

📊 A universal enrichment tool for interpreting omics data

Gene Set Enrichment Analysis in Python

CellRank: dynamics from multi-view single-cell data