A BioGem to submit jobs on a queue system

Enables programmatic parsing of HMMER version 3 reports

Parse PFAM HMM definition files so that the models can be accessible programmatically

Reads metadata from Integrated Microbial Genomes (IMG) metadata files into a programmaticly useful state.

A Jruby wrapper to Incanter lib

BioInterchange is a Ruby gem, command-line tool, web-service for turning heterogeneous data formats such as JSON, XML, GFF3, etc., into RDF."

a programmatic interface to the iPCRess in-silico PCR software. iPCRess is part of the exonerate suite.

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

Basic wrapper for the Kallistio Mapper

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.

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

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

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, KEGG REST API, NCBI E-Utilities, and GenomeNet(genome.jp).

Tools to find similarity between pangenomes.

Provides PhyloXML support for BioRuby.

Iterate through a samtools pileup file

Methods for handling multiwell plate annotations, includes ranges and quadrants