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Mark Chen's Projects

atacseq icon atacseq

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

awesome-pipeline icon awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

awesome-single-cell icon awesome-single-cell

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

blog icon blog

Personal blog built by blogdown.

chipseq icon chipseq

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

conga icon conga

Clonotype Neighbor Graph Analysis

gansha icon gansha

Data analyses for project MC010.

gorthor icon gorthor

R package to access gOrtholog - an orthology database

hgvs icon hgvs

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

rmarkdown-book icon rmarkdown-book

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

rnaseq icon rnaseq

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

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