8 open source projects by aertslab

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

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.

A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.

AUCell: score single cells with gene regulatory networks

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

GENIE3 (GEne Network Inference with Ensemble of trees) R-package

Fast visualization tool for large-scale and high dimensional single-cell data

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data