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).

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@tg...

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

A dead simple method of running shell commands from within Ruby, by applying opinion

Bioruby core plugins

BioRuby plugins with dependecies from external library or tools

Restriction Enzyme Dataset from REBASE in yaml form

Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags

decoding the dbSNP bitfield containg detaild information

a method to get the nucleotide sequence of translations done by the EMBOSS bioinformatics package program transeq.

This API provides a complete set of methods and classes to access the Ensembl database using Ruby programming language

A Ruby library for the RESTful Ensembl API.

Parse publications for gene names in a fuzzy fashion

Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins. Requires local install of the program, which is available from http://bioinf.wehi.edu.au/exportpred/

Interface for express beta diversity file formats

ools to work with fasta files, indexed with samtools. The initial releases depend on bio-samtools, but that will change