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

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 mutations.