ChIP-seq analysis notes from Ming Tang

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

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

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs

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

ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnrich provide functions to import any in-house catalogue, automate and plot the enrichment analysis for genomic regions.

Ⓜ️ Tool for motif conservation analysis

Python bindings for the TFM-Pvalue program.

An R package for de novo discovery of enriched DNA motifs (e.g. TFBS)

Motif discovery for DNA sequences using multiobjective optimization and genetic programming.

Scripts for motif assessment for HOCOMOCO v10/v11.

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.

Dual threshold optimization for identifying convergent evidence: TF binding locations and TF perturbation responses.

Prediction of the binding specificity of transcription factors using support vector regression

DNA Transcription Factor Binding Prediction (Self-learning Project)

A robust statistical test for TF footprint data analyses

Threshold and p-value computations for Position Weight Matrices