Brad Chapman

Login: chapmanb

Company: Harvard Chan Bioinformatics Core

Location: Boston, MA

Bio: Biologist and programmer

Blog: http://bcb.io

Blog: http://bcb.io

Member of

1. AstraZeneca - NGS Team
2. BD2K Center for Translational Genomics
3. Biopython Project
4. biosql
5. Blue Collar Bioinformatics
6. Common Workflow Language
7. conda-forge
8. Harvard Chan School: Bioinformatics Core
9. Intergalactic Utilities Commission
10. ISA tools
11. MultiQC
12. null
13. null
14. null
15. null

Repositories

arvados

an open source platform for managing and analyzing biomedical big data

bazel-feedstock

A conda-smithy repository for bazel.

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bcbio.adam

Experiment: Clojure interface to ADAM distributed file formats for variants and aligned reads

bcbio-conda

Deprecated conda recipes for bcbio python code and dependencies -- migrated to bioconda

bcbio.coverage

Investigate coverage metrics for variant calling experiments

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines

bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines

bcbio.pipeline

Next-generation sequencing analysis pipelines built on Hadoop and Cascalog

bcbio.prioritize

Prioritize small variants, structural variants and coverage based on biological inputs

bcbio.run

Idempotent, transactional runs of external command line programs

bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure

bcbio.variation.plus

Extended functionality for analyzing genomic variability, built on bcbio.variation and GATK

bcbio.variation.recall

Parallel merging, squaring off and ensemble calling for genomic variants

bioblend

A python library for interacting with CloudMan and Galaxy API

bioconda-recipes

Conda recipes for the bioconda channel.

bio.ensembl

Clojure API for Ensembl data access via JEnsembl

biopython

Brad's fork of main repository

bioruby-vcf

Smart VCF parser

biosqlweb

BioSQL web

c2

Declarative data visualization in Clojure(Script).

CAGe

Changepoint Analysis of Genomic Reads

cgpBattenberg

Battenberg algorithm and associated implementation script

chapmanb.github.com

null

ChromosomeMappings

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

CircDesigNA

Multimolecular NA Design tool with support for extensible sequence constraints

clj-blend

Clojure library for interacting with Galaxy, CloudMan, and BioCloudCentral, built on blend4j

clj-gcon

Genome Connector: Clojure API to access multiple genomic resources

clj-genomespace

Access GenomeSpace data integration platform with simple Clojure API

cljs-chosen

ClojureScript interface to Harvest's Chosen library

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

cnvkit

Copy number variant detection from targeted DNA sequencing

colormath-feedstock

A conda-smithy repository for colormath.

common-workflow-language

Repository for CWL Specfications

conda-recipes

build and test recipes for conda

cwl2wdl

Convert CWL to WDL

cwltool

Common Workflow Language reference implementation

cyvcf

A fast Python library for VCF files leveraging Cython for speed.

cyvcf2

cython + htslib == fast VCF parsing

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

delly

DELLY: Structural variant discovery by integrated paired-end and split-read analysis

DKFZBiasFilter

null

dotfiles

~chapmanb dotfile organization for backup and sychronization

dx-cwl

Import and run CWL workflows on DNAnexus (alpha)

elasticluster

null

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

galaxy-hub

Galaxy Community Hub

gatk

GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses

gatk-1

Official code repository for GATK versions 4 and up

gemini

a lightweight db framework for disease and population genetics.

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

gkno_launcher

The gkno launcher for executing tools or pipelines

glia

a string to graph aligner

goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

grabix

a wee tool for random access into BGZF files.

gvcf_regions

null

homebrew

The missing package manager for OS X.

homebrew-cbl

Homebrew repository for CloudBioLinux: incubator for formulas to end up in homebrew-science

homebrew-science

Scientific formulae for the Homebrew package manager

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

joblib

Python function as pipeline jobs.

kwd-doc-find

Clojure web server providing full-text document searching via Lucene

linuxbrew

A fork of Homebrew for Linux

loftee

null

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

manta

Structural variant and indel caller for mapped sequencing data

metasv

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing

mgh_projects

In-progress code for various research projects

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

mypubs

creation of methods with the purpose of tools comparison

ncbi-hackathons.github.io

NCBI Hackathon Repos

o8

Genetic changes we can believe in: a web based tool for variant visualization and analysis

octopus

Bayesian haplotype-based mutation calling

oswitch

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

Platypus

Platypus Variant Caller

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

pysam

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

python-graph

Automatically exported from code.google.com/p/python-graph

PyVCF

A Variant Call Format reader for Python.

richard-deploy

some fabric scripts for Carl to deploy a pyvideo site

RNA-SeQC

null

rust-bio.github.io

Github pages for Rust-Bio

r-var

Exploring our genomic variability

sambamba

Tools for working with SAM/BAM data

samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.

samtools

null

schema_salad

Semantic Annotations for Linked Avro Data

sciclone

An R package for inferring the subclonal architecture of tumors

scipy2013_talks

Content presented at the 2013 SciPy conference

simple_sv_annotation

Simplify snpEff annotations for interesting cases

smash

Benchmarking toolkit for variant calling

smoove

structural variant calling and genotyping with existing tools, but, smoothly.

SnpEff

null

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

svtyper

Bayesian genotyper for structural variants

TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

toil

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python

umis

Tools for processing UMI RNA-tag data

VarDict

VarDict

VarDictJava

VarDict Java port

VariantBam

Filtering and profiling of next-generational sequencing data using region-specific rules

vcf2db

create a gemini-compatible database from a VCF

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

vcfgo

a golang library to read, write and manipulate files in the variant call format.

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

vcftools-cpan

cpanm ready distribution of VCFtools Perl libraries

vt

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

wham

Structural variant detection and association testing

zeromq-feedstock

A conda-smithy repository for zeromq.

Commits To

Repository	Most Recent Commit	# Commits
chapmanb/r-var	2011-09-19 01:20:26.0	60
hbc/projects	2017-10-22 10:04:29.0	382
chapmanb/bcbio.variation	2015-11-02 09:38:14.0	996
galaxyproject/bioblend	2013-05-30 01:13:14.0	4
chapmanb/bcbio.variation.recall	2016-08-15 16:27:51.0	92
hall-lab/svtyper	2015-08-17 10:04:13.0	1
wurmlab/oswitch	2015-06-08 00:36:26.0	1
bcbio/bcbio.github.io	2017-03-27 10:33:56.0	22
ISA-tools/bioconda-recipes	2018-01-11 14:11:51.0	35
brentp/smoove	2018-03-21 15:07:13.0	1

---

• NIH
• NCATS
• CTSA
• CD2H
• CD2H Labs

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.