Transcription Factors Python Packages

pyscenic

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.

pyjaspar

pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs

tf-bind-transformer

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

scregulate

Python Toolkit for Transcription Factor Activity Inference and Clustering of scRNA-seq Data

moca

Tool for motif conservation analysis

netzoopy-sponge

A package to generate prior gene regulatory networks.

netzoopy

netZooPy is a network biology package implemented in Python.

mamotif

An integrative toolkit for detecting cell type-specific regulators

motifscan

A motif discovery tool to detect the occurrences of known motifs

pyscorpion

Constructs cell-type-specific gene regulatory networks from single-cell RNA-sequencing data using the SCORPION algorithm, which aggregates cells into super-cells and applies PANDA to infer transcription factor-target regulatory relationships.

transfacpred

A method to predict the transcription factors using protein sequences.