Brad Chapman

bcbb. Incubator for useful bioinformatics code, primarily in Python and R

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

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

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

o8. Genetic changes we can believe in: a web based tool for variant visualization and analysis

biosqlweb. BioSQL web

clj-blend. Clojure library for interacting with Galaxy, CloudMan, and BioCloudCentral, built on blend4j

r-var. Exploring our genomic variability

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

bcbio.prioritize. Prioritize small variants, structural variants and coverage based on biological inputs

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

bcbio.pipeline. Next-generation sequencing analysis pipelines built on Hadoop and Cascalog

dotfiles. ~chapmanb dotfile organization for backup and sychronization

zmk-34key-split.

clj-gcon. Genome Connector: Clojure API to access multiple genomic resources

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

bcbio.run. Idempotent, transactional runs of external command line programs

gvcf_regions. Python

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

kwd-doc-find. Clojure web server providing full-text document searching via Lucene

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

samtools. C

zmk-architeuthis-dux. ZMK keyboard firmware shield for Architeuthis Dux

conda-recipes. build and test recipes for conda