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

Using CNNs to model affect of histone modification on gene expression

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

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

Usage analysis of histone post-translational modifications using msqrob2PTM

JEDIpy: Joint Epi-transcriptomics Dynamics Inference in Python

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

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.

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.

Practical and home works in the discipline Bioinformatics.