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Brad Chapman's Projects

arvados icon arvados

An open source platform for managing and analyzing biomedical big data

bcbb icon bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bcbio-conda icon bcbio-conda

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

bcbio.adam icon bcbio.adam

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

bcbio.pipeline icon bcbio.pipeline

Next-generation sequencing analysis pipelines built on Hadoop and Cascalog

bcbio.prioritize icon bcbio.prioritize

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

bcbio.run icon bcbio.run

Idempotent, transactional runs of external command line programs

bcbio.variation icon bcbio.variation

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

bcbio.variation.plus icon bcbio.variation.plus

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

bioblend icon bioblend

A python library for interacting with CloudMan and Galaxy API

c2 icon c2

Declarative data visualization in Clojure(Script).

cage icon cage

Changepoint Analysis of Genomic Reads

chromosomemappings icon chromosomemappings

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

circdesigna icon circdesigna

Multimolecular NA Design tool with support for extensible sequence constraints

clj-blend icon clj-blend

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

clj-gcon icon clj-gcon

Genome Connector: Clojure API to access multiple genomic resources

clj-genomespace icon clj-genomespace

Access GenomeSpace data integration platform with simple Clojure API

cljs-chosen icon cljs-chosen

ClojureScript interface to Harvest's Chosen <select> library

cloudbiolinux icon cloudbiolinux

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

cnvkit icon cnvkit

Copy number variant detection from targeted DNA sequencing

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