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, KE...

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

Server for polymarker. To be used with cron

Primer3-related Ruby code - wrappers, Boulder IO, etc.

Bio::Protparam has same interface and function as Bio::Tools::Protparam class of BioPerl, except that it calculate parameters instead of throwing query to Expasy protparam tool.

A toolkit for publishing scientific results and datasets using RDF, OWL, and related technologies

Just a test

Store relationships in a triple-store, such as gene enrichment and QTL, and use this information for inference and causality

Provides PhyloXML support for BioRuby. This bioruby-phyloxml gem replaces old unmaintained bio-phyloxml gem.

Simple classes for parsing SAM, CIGAR and MD:Z strings, including slices. Methods for calling mutations in HGVS format and looking up consequences using Ensembl VEP REST API. Developed for calling mutations at an expected position in an alignment - e.g. Amplicon sequencing of CRISPR-induced mutat...

A minimal web service on the top of sinatra to query bam files

BioRuby Shell is a command line interface on BioRuby open source bioinformatics library. It provides easy-to-use analysis environment for bioinformatics.

A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least.

A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA metadata) SQLite database.