A quick and dirty tool for analysis of transition and transversion frequency aross and alignment

GEM to annotate bacterial genome sequence based on a reference genome and complete the annotation with an external database.

A simple biogem that allows computation of the aliphatic index of a protein

bioruby plugin to parse, write, and manipulate assembly data

bioruby plugin to parse, write, and manipulate assembly data

Data mining and machine learning algorithms for JRuby

Meta package for BioLinux distribution: bio-core, bio-core-ext

Provides BioSQL support for BioRuby.

Ruby script for data-mining biostars.org using web-crawling techniques as well as utilizing the Biostars RESTful API. Statistical analysis requires R (http://www.r-project.org).

Extract the sequence of the subjects' region based on blast search.

BioRuby BLAST XMLParser plugin: a plugin of BioRuby BLAST XML result parser by using the XMLParser extension. This was formerly a part of the BioRuby core ("bio" gem) and split to this gem because of the external XMLParser dependency.

Tools to manipulate blat files from the command line. Uses the Bio::Blat object from BioRuby, but the parser has been modified to avoid reading the whole psl file, it yields just the current entry and it is up to the consumer to decide to store it or not." s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"

Ruby binding for BWA mapping software, built using Ruby-FFI library

A Ruby library for reading CD-HIT cluster reports

BioRuby plugin for ChEMBL REST API Client, Parser and Container classes

A parser for CIGAR format alignments.

Programmatic interface to the cNLS nuclear localisation signal prediction software

Bioruby core plugins

Bioruby core plugins

BioRuby plugins with dependecies from external library or tools