Incubator for useful bioinformatics code, primarily in Python and R

My personal collection of R scripts.

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

My collection of bite size tools for some bioinformatics routines.

matplotlib: plotting with Python

A powerful toolset for genome arithmetic.

Python library to facilitate genome assembly, annotation, and comparative genomics

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

Core BioPerl 1.x code

Find nodes in hierarchical clustering that are statistically significant

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Official git repository for Biopython (originally converted from CVS)

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 1…