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Incubator for useful bioinformatics code, primarily in Python and R

branch: master
Octocat-spinner-32 align Avoid converting to and from phred format for speed December 16, 2010
Octocat-spinner-32 biopython Coding region coordinate remapping for SNPs June 18, 2010
Octocat-spinner-32 biosql SQLAlchemy definitions for BioSQL; partial implementation August 21, 2009
Octocat-spinner-32 biosql_ontologies Finalized initial version December 14, 2008
Octocat-spinner-32 biostar Supporting code and configuration for BioStar NGS challenge from Pierre December 19, 2011
Octocat-spinner-32 classify Move Dan's scripts to separate project directory in mgh_projects May 17, 2011
Octocat-spinner-32 distblast Remove num_alignments, since it's incompatible (and redundant) with m… December 09, 2013
Octocat-spinner-32 galaxy Initial move of next gen automated analysis into git revision control September 01, 2010
Octocat-spinner-32 gff Handle unescaped semi-colons within quotes and add test case. #83 March 12, 2014
Octocat-spinner-32 keyval_testing Update couchdb test with bulk loading fixed from Paul and Chris May 11, 2009
Octocat-spinner-32 nextgen Add update notice about new bcbio-nextgen repository February 06, 2013
Octocat-spinner-32 papers Update chapman_bcbio.tex December 10, 2013
Octocat-spinner-32 posts Post on bcbio-nextgen-vm: docker + bcbio-nextgen March 06, 2014
Octocat-spinner-32 qualbin Add plot for variant cause changes February 12, 2013
Octocat-spinner-32 rest_apis Move Dan's scripts to separate project directory in mgh_projects May 17, 2011
Octocat-spinner-32 semantic Update query example to match paper text April 30, 2012
Octocat-spinner-32 stats Updated script for bootstrapping R November 22, 2010
Octocat-spinner-32 talks Slides for ABCD talk April 17, 2014
Octocat-spinner-32 validation Add nice labels for identifying callers October 15, 2013
Octocat-spinner-32 visualize Move Dan's scripts to separate project directory in mgh_projects May 17, 2011
Octocat-spinner-32 .gitignore Initial work on bcbio-nextgen talk for BOSC 2013 July 12, 2013
Octocat-spinner-32 README.md Add update notice about new bcbio-nextgen repository February 06, 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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