markgene

Pinned Repositories

atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
Language:Nextflow0 1 00
ATACseqQC
ATAC-seq Quality Control
Language:R0 1 00
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
0 2 00
cutnrun
CUT&RUN pipeline
Language:Nextflow1 2 00
maxprobes
Methylation Array Cross-Reactive Probes
Language:R4 2 11
yamatClassifier
Yet Another Methylation Array Toolkit: Classifier
Language:R1 2 00

markgene's Repositories

markgene/cutnrun
CUT&RUN pipeline
Language:Nextflow1 2 00
markgene/yamatClassifier
Yet Another Methylation Array Toolkit: Classifier
Language:R1 2 00
markgene/atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
Language:Nextflow0 1 00
markgene/ATACseqQC
ATAC-seq Quality Control
Language:R0 1 00
markgene/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
1 0
markgene/blog
Personal blog built by blogdown.
Language:HTML2 0
markgene/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
Language:Nextflow1 0
markgene/conga
Clonotype Neighbor Graph Analysis
Language:Jupyter Notebook1 0
markgene/cv
Mark's CV
Language:TeX1 0
markgene/gansha
Data analyses for project MC010.
Language:Nextflow2 0
markgene/GenVisR
Genome data visualizations
Language:R2 0
markgene/hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Language:Python0 0
markgene/hgvs-nomenclature
markgene/mac-config
Config Mac
Language:Shell2 0
markgene/markgene
Config files for my GitHub profile.
1 0
markgene/markgene.github.io
Mark Chen's GitHub Pages
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markgene/MC015_Persister_public
Language:R2 01
markgene/MC130_snvannotators
Language:Python
markgene/mutils
Language:R2 0
markgene/pyoncokb
Language:Python
markgene/r4ds
R for data science
Language:R2 0
markgene/rmarkdown-book
R Markdown: The Definitive Guide (published by Chapman & Hall/CRC in July 2018)
Language:RMarkdown1 0
markgene/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Language:Nextflow1 0
markgene/snvannotators
Language:Python
markgene/snvmodels
Language:Python
markgene/transcriptfeatures
Language:Python
markgene/Windows
Config WIndows
1 0
markgene/yamat
Yet Another Methylation Array Toolkit
Language:R2 0
markgene/yamatCN
Yet Another Methylation Array Toolkit: Copy Number Analysis Module
Language:R2 0
markgene/Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
Language:Jupyter Notebook1 0