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).

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"

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

A Ruby library for the RESTful Ensembl API.

BioRuby executables is a collection of miscellaneous utilities for bioinformatics that were formerly part of the BioRuby core ("bio" gem). Because of reducing complexity, they were moved to this gem.

Parse publications for gene names in a fuzzy fashion

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

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

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).

Ruby wrapper for the gff3-pltools.

A Ruby client for GGGenome the Ultrafast sequence search

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