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

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@tgac.ac.uk"

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

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

Programmatic interface to the cNLS nuclear localisation signal prediction software

Bioruby core plugins

BioRuby plugins with dependecies from external library or tools

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.

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/

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

ruby parser for FastQC, a quality control software for high-throughput sequencing data.

longer description of your gem

bio-gag is a biogem for detecting and correcting a particular type of error that occurs/occurred in particular versions of the IonTorrent DNA sequencing kit. Recent versions of the system don't appear to suffer the same problem

Bioinformatics. Aggregate FastQC (quality control for Next Generation Sequencing -NGS-) results from many different samples in a single web page, with charts and tables organized and simplified. The main goal is to speed up the communication process with colleagues (PIs, Biologists, BioInformaticians).

GFF3 (genome browser) information and digest mRNA and CDS sequences. Options for low memory use and caching of records. Support for external FASTA files.

Identify causative mutations in a model genome from NGS reads using the NGM method.

Encode any message string into a DNA sequence