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.

Single-cell Transcriptome and Regulome Analysis Pipeline

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

netZooR is a network biology package implemented in R.

🎯 Human transcription factor target genes from 6 databases in convenient R format.

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

netZooPy is a network biology package implemented in Python.

Netbooks is a JupyterHub catalog of use cases in gene regulatory network inference using netZoo methods..

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

netZooM is a network biology package implemented in MATLAB.

netZooC is a network biology package implemented in C.

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs

Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.

A motif discovery tool to detect the occurrences of known motifs

Read HOMER motif analysis output in R.

Deep neural networks implemented in TensorFlow & Python for predicting whether transcription factors will bind to given DNA sequences

Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data

MYB transcription factors are one of the largest gene family in plants and control many processes. This repository provides additional background to the #MYB_Monday tweets

A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.