Gene Regulation Python Packages

pyjaspar

pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs

arboreto

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

circe-py

Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.

tfbs-footprinting

Pipeline: Identification of cis-regulatory elements by matrix scoring and conservation.

tfbs-footprinting3

Tool for identifying conserved TFBSs in vertebrate species.

omnipath-client

Python client for the new OmniPath web APIs

mamotif

An integrative toolkit for detecting cell type-specific regulators

improse

Integrated workflow to predict super-enhancers and compute feature importance