Basic tools for parsing, searching, and comparing JASPAR motifs; Based on Bio.motifs module in Biopython

Basic wrapper for the Kallistio Mapper

Provide access to the IlluminaHumanAnnotations. Database comes form Bioconductor's package lumiHumanIDMapping

A biogem for counting small kmers for fingerprinting nucleotide sequences. See README for details.

This biogem is built around Krona, a flashy way of representing hierarchical data.

This is very scrappy at the moment, and will need to be seriously cleaned up. It does what I need it to do for now. I'll fix it up in the coming weeks. Promise :)

Simple, under development Ruby solution for UCSC LiftOver tool

This is a BioRuby plugin providing FALDO location RDF output method for Bio::Location objects. A method Bio::Location#rdfize is added.

Log4r wrapper for BioRuby

Client package for creating, sending, recieving and consuming SOAP messages from BioModels search engine

Help for working with the output of the .delta files produced by nucmer and promer

Running and parsing of the protein transmembrane domain predictor octopus

Emulator that emulates Bio::Fetch object in BioRuby as if old BioRuby BioFetch server were still alive. It overrides methods and objects in Bio::Fetch, and if the old BioRuby BioFetch server's URL is given, it intercepts all requests and converts them into existing web services such as TogoWS, KE...

Provides PhyloXML support for BioRuby.

Pipeline to remove contaminations from EST libraries

Iterate through a samtools pileup file

The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptides in Plasmodium falciparum. This is an implementation of that algorithm.

Methods for handling multiwell plate annotations, includes ranges and quadrants

Server for polymarker. To be used with cron

Primer3-related Ruby code - wrappers, Boulder IO, etc.