Matt Shirley

Login: mdshw5

Company: @novartis

Location: Cambridge, MA

Bio: Computational biologist. Oncology, and rare disease genetics. Python user.

Blog: http://mattshirley.com

Blog: http://mattshirley.com

Member of

1. Johns Hopkins University Center for Computational Genomics

Repositories

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

bioconda-recipes

Conda recipes for the bioconda channel.

bioc-refcard

Bioconductor quick reference card / cheat sheet

biopython

Official git repository for Biopython (converted from CVS)

bsseq

Devel repository for bsseq

cellranger

10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

cnvkit

Copy number variant detection from targeted DNA sequencing

Complete-Striped-Smith-Waterman-Library

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CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

cufflinks

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docker-unifi

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dotfiles

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fastqp

Simple FASTQ quality assessment using Python

FreePSI

An alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome

galaxy

Data intensive biology for everyone.

galaxy-json-data-source

Data source tool for importing multiple datasets using a JSON schema

gemini

a lightweight db framework for disease and population genetics.

gffutils

GFF and GTF file manipulation and interconversion

hamstring

Tools for generating and decoding error-correcting DNA barcodes

hap.py

Haplotype VCF comparison tools

htslib

C library for high-throughput sequencing data formats

hts-python

pythonic wrapper for libhts

hy

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iSEE

R/shiny interface for interactive visualization of data in objects derived from the SummarizedExperiment class

lecture-notes

Lecture notes and example files for FAES BIOF309 Python course

linux

Linux kernel source tree

mattshirley.com

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mendelianerror

probability of mendelian error in trios.

ncbi-vdb

ncbi-vdb

ngg2

Python script to identify NGGNGG Cas9 gRNA sites in any indexed FASTA file.

ngs

NGS Language Bindings

od-forum-code-of-conduct

Code of Conduct for CoA-hosted online forums

pevsner_lab

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posts

blog posts for mattshirley.com

pyensembl

Python interface to ensembl reference genome metadata (exons, transcripts, etc...)

pyfaidx

Efficient pythonic random access to fasta subsequences

pypette

Ridiculously simple flow controller for building complex pipelines

RapClust

Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes

salmon

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

simplesam

Simple pure Python SAM parser and objects for working with SAM records

snp-flip

Simple command line tool reporting the reverse strand SNPs in your GWAS data.

squid

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sra-tools

SRA Tools

sra-tools-galaxy

NCBI SRA toolkit Galaxy package and tool wrappers

strandex

Sample an approximate number of reads from a fastq file without reading the entire file

tripod

Sensitive detection of chromosomal abnormalities in parent-child trio-based microarray data.

tripod-web

web application for triPOD detection

UniFi-Video-Controller

Docker for Unifi-Video Controller (Ubiquiti Networks)

VCF-kit

VCF-kit: Assorted utilities for the variant call format

vt

A tool set for short variant discovery in genetic sequence data.

Commits To