transcription-factor-binding 开源项目推荐（42 个）

crazyhottommy /ChIP-seq-analysis

Ming Tang 的 ChIP-seq 分析笔记

MAGICS-LAB /DNABERT_2

[ICLR 2024] DNABERT-2：面向多物种基因组的高效基础模型与基准

lucidrains /tf-bind-transformer

一个探索使用 transformer 预测 DNA ↔ 转录因子结合的仓库

pinellolab /haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

MiraldiLab /maxATAC

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

tanjimin /Chromnitron

A multimodal model predicting chromatin-associated proteins binding on the human genome.

Danko-Lab /rtfbs_db

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

remap-cisreg /ReMapEnrich

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.

j-andrews7 /pytfmpval

Python bindings for the TFM-Pvalue program.

saketkc /moca

Ⓜ️ Tool for motif conservation analysis

MyersGroup /MotifFinder

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

mbelmadani /motifgp

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

Huising-Lab /epiRomics

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.

BrentLab /Dual_Threshold_Optimization

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

VorontsovIE /diHOCOMOCO

Scripts for motif assessment for HOCOMOCO v10/v11.

asntech /jaspar

Source code for JASPAR web portal and REST API

kchu25 /MotifPvalue.jl

Threshold and p-value computations for Position Weight Matrices

mahossam /DNA-Transcription-Factor-Binding-Prediction

DNA Transcription Factor Binding Prediction

draeger-lab /SABINE

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

UcarLab /BiFET

A robust statistical test for TF footprint data analyses