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.

Parses stockholm sequence alignment format

Tabix file indexing routines from the samtools package http://samtools.sourceforge.net/

A bioruby plugin for interaction with the transmembrane predictor TMHMM

Ruby FFI binding of the ucsc kent src. Implemented utilities include: bigWigInfo, bigWigSummary and wigToBigWig

BioRuby plugin for UniChem REST Web service

Parser to work with some file formats used in the velvet DNA assembler