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.

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

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

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

Using CNNs to model affect of histone modification on gene expression

Cell type-specific Histone Acetylation Score

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

Practical and home works in the discipline Bioinformatics.

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)

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

my master's research in bioinformatics

A technical note to describe the segmenter package

Preprocessing pipeline for CUT&TAG data.

A nucleosomal reads counting tool

ChIP-seq normalization according to background reads density. (R package)

Independent project I undertook to perform a full ChIP-Seq analysis of the transcription factor Nanog in Zebrafish embryos.

Gene expression prediction with Convolutional Recurrent Neural Networks