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.

Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR

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.

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

Artificial neural network to predict transcription factor binding.