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Incubator for useful bioinformatics code, primarily in Python and R
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abstracts Finalize bcbio CWL abstract for BOSC Apr 4, 2016
align Avoid converting to and from phred format for speed Dec 16, 2010
biopython Coding region coordinate remapping for SNPs Jun 18, 2010
biosql SQLAlchemy definitions for BioSQL; partial implementation Aug 21, 2009
biosql_ontologies Finalized initial version Dec 14, 2008
biostar Supporting code and configuration for BioStar NGS challenge from Pierre Dec 19, 2011
classify Move Dan's scripts to separate project directory in mgh_projects May 17, 2011
cv CV and research statement: clean up typos and improve phrasing Apr 8, 2015
distblast Remove num_alignments, since it's incompatible (and redundant) with m… Dec 9, 2013
galaxy Initial move of next gen automated analysis into git revision control Sep 1, 2010
gff Add note about using gffutils May 30, 2016
keyval_testing Update couchdb test with bulk loading fixed from Paul and Chris May 11, 2009
nextgen Add update notice about new bcbio-nextgen repository Feb 6, 2013
papers/bcbio-nextgen Update chapman_bcbio.tex Dec 10, 2013
posters Poster from Luca on bcbio-nextgen for cancer calling Jun 21, 2014
posts Conference notest from AWS Life Sciences Day 2016 May 17, 2016
qualbin Add plot for variant cause changes Feb 12, 2013
rest_apis Move Dan's scripts to separate project directory in mgh_projects May 17, 2011
semantic Update query example to match paper text Apr 30, 2012
stats Updated script for bootstrapping R Nov 22, 2010
svplot Generalize SV circos-style plots with multi depth Jan 8, 2016
talks Teaching materials for NGS long course variant calling Apr 28, 2016
validation Update scalpel results with improved filtering and include suggestion… Jan 5, 2015
visualize Move Dan's scripts to separate project directory in mgh_projects May 17, 2011
.gitignore Presentation for Intel Life Sciences tutorial Aug 7, 2014
README.md Add update notice about new bcbio-nextgen repository Feb 6, 2013

README.md

Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics.

Some projects which may be especially interesting:

  • CloudBioLinux -- An automated environment to install useful biological software and libraries. This is used to bootstrap blank machines, such as those you'd find on Cloud providers like Amazon, to ready to go analysis workstations. See the CloudBioLinux effort for more details. This project moved to its own repository at https://github.com/chapmanb/cloudbiolinux.
  • gff -- A GFF parsing library in Python, aimed for inclusion into Biopython.
  • nextgen -- A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. This project has moved into its own repository: https://github.com/chapmanb/bcbio-nextgen
  • distblast -- A distributed BLAST analysis running for identifying best hits in a wide variety of organisms for downstream phylogenetic analyses. The code is generalized to run on local multi-processor and distributed Hadoop clusters.
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