histone-modifications

ChIP-seq analysis notes from Ming Tang

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

🧬 🦀 A fast and efficient tool to perform a genome wide Single cell Chromatin State Analysis using multimodal histone modification data.

A unified framework for discovering, analyzing, integrating, and visualizing regulatory motifs and transcription factor binding sites across bulk, single-cell, and long-read sequencing modalities.

Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility

ChIP-seq analysis: QC and contamination screening, Bowtie2 alignment, MACS2 broad peaks, DiffBind, and monaLisa/JASPAR motif enrichment, with a MultiQC report.

This is a R package that intends to perform all the features possible by tensor decomposition based unsupervised feature extraction

geneSpark is a bioinformatics software program written in Python and Apache Spark for big data epigenetic histone modification ChIP-seq analysis.

Processing, benchmarking and analysis of CUT&Tag against ENCODE ChIP-seq.

Cell type-specific Histone Acetylation Score

A method for predicting chromatin features and prioritizing non-coding rice variants using DNA language models.

Using CNNs to model affect of histone modification on gene expression

Sperm-derived H2AK119ub1 is required for embryonic development in Xenopus laevis

Usage analysis of histone post-translational modifications using msqrob2PTM

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.

geneXtendeR analysis on 198 human histone modification ChIP-seq ENCODE datasets

Practical and home works in the discipline Bioinformatics.

The abstract and poster for my internship under the Stanford Institutes of Medical Research at the Khatri Lab in the summer of 2019. More code/scripts can be made available upon request (I used primarily R and SQL)

Documenting my progress towards discovering relevant determinants and better understanding the mechanisms and limitations of KLF4 pioneer factor ability as well as establishing familiarity with the nucleosome/histone/chromatin environment.

Gene expression prediction from histone modification marks using CNN and BiLSTM +Attention