Fasta reader, ORF emitter, sequence translation

Fast big data BLAST XML parser and library; this libxml2 based version is 50x faster than BioRuby and comes with a nice CLI

Multiple Alignment Format parser for BioRuby.

Functions and tools for tranforming and changing tab delimited and comma separated table files - useful for Excel sheets and SQL/RDF output

A dead simple method of running shell commands from within Ruby, by applying opinion

Bioruby core plugins

Interface for express beta diversity file formats

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

GFF3 (genome browser) information and digest mRNA and CDS sequences. Options for low memory use and caching of records. Support for external FASTA files.

Enables programmatic parsing of HMMER version 3 reports

A biogem for counting small kmers for fingerprinting nucleotide sequences. See README for details.

Iterate through a samtools pileup file

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

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

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.

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

Bindings to some internals of the velvet assembler.

FPKG (gene expression metric) calculator for metatranscriptomics

divvy up spectra from DTASelect files in a somewhat parsimonious way