Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Useful bioinformatics code, primarily in Python and R
Branch: master
Pull request Compare This branch is 1063 commits behind chapmanb:master.

Fetching latest commit…

Cannot retrieve the latest commit at this time

Failed to load latest commit information.
align
biopython
biosql
biosql_ontologies
classify
distblast
ec2
galaxy
gff
keyval_testing
nextgen
rest_apis
semantic
stats
visualize
.gitignore
README.md

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:

  • ec2 -- 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.
  • gff -- A GFF parsing library in Python, aimed for inclusion into Biopython.
  • nextgen -- Automated analysis pipeline for processing next generation sequencing data. This is tightly integrated with the Galaxy web framework.
  • 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.
Something went wrong with that request. Please try again.