markgene

maxprobes

Methylation Array Cross-Reactive Probes

cutnrun

CUT&RUN pipeline

atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

ATACseqQC

ATAC-seq Quality Control

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

blog

Personal blog built by blogdown.

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

clonotracker-cl

ClonoTracker command line

conga

Clonotype Neighbor Graph Analysis

cv

Mark's CV

gansha

Data analyses for project MC010.

GenVisR

Genome data visualizations

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

hgvs-nomenclature

hugo-user-page

My Hugo User Page

mac-config

Config Mac

markgene

Config files for my GitHub profile.

markgene.github.io

Mark Chen's GitHub Pages

MC015_Persister_public

mutils

r4ds

R for data science

rmarkdown-book

R Markdown: The Definitive Guide (published by Chapman & Hall/CRC in July 2018)

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Windows

Config WIndows

yamat

Yet Another Methylation Array Toolkit

yamatClassifier

Yet Another Methylation Array Toolkit: Classifier

yamatCN

Yet Another Methylation Array Toolkit: Copy Number Analysis Module

Zika-RNAseq-Pipeline

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study