netZooR is a network biology package implemented in R.

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

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.

Single Cell Oriented Reconstruction of PANDA-based Individually Optimized Networks

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

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

Read HOMER motif analysis output in R.

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

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

Analysis of Single Molecule Footprinting (SMF) data for the analysis of DNA methylation, chromatin accessibility and TF binding. The repository contains all primary code to reproduce the main analyses for the publication "Single molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation" (Kreibich et al., 2023)

An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. epiRomics is also designed to identify enhancer and enhanceosome regions from these data.

⚠️ ARCHIVED ⚠️ An R package to access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer

The repository contains all the scripts necessary for the bioinformatic characterisation of the IDRs of Arabidopsis transcription factors.

CMTCN: A web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks

Identification of enriched motif pairs from chromatin interaction data

Code and resources related to the olfactory regeneration project

ForkedTF is an R-library that introduces Forked-PMW (FPMW) and Forked-Sequence Logos (F-Logos) to provide a more comprehensive depiction of the sequence affinity of a Transcription factor (TF) of interest, including its DNA sequence and DNA methylation level, along with a segregated list of partner TFs.

This is the fork of the Bioconductor-mirror repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/chipenrich.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=chipenrich.

miRinGO: Prediction of GO terms indirectly targeted by human microRNAs

An R package to access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer