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..

Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.

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.

In Press, GigaScience. Web app for post-GWAS/QTL analysis that performs a slew of novel bioinformatics analyses to cross-reference GWAS/QTL mapping results with a host of publicly available rice databases

This is a small database of 165 manually-reviewed MADS-box family transcription factors in plants.

Anchor Residue Identification

An ensemble method for predicting transcription factor in protein sequences

Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

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

All code generated for Loupe et al. 2023

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.

netZooR is a network biology package implemented in R.

CRAFT: Cellular Reprogramming Analysis with Integrated Framework and Mechanistic Insight

pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs

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

Shiny app for screening for core promoter occurrences close to expressed transposons TSSs.

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