Affymetrix microarray file format parser (CEL/CDF) for Ruby. FFI binding to Biolib port of R/Affyio by Benjamin Milo Bolstad

Data mining and machine learning algorithms for JRuby

This library provides support for BGZF (Blocked GZip Format) in Ruby. BGZF, originally defined as part of the SAM/BAM specification, is used to compress record-oriented data in a way that facilitates random access, unlike plain gzip. BGZF is principally used for bioinformatics data but would be u...

Fasta reader, ORF emitter, sequence translation

Extract the sequence of the subjects' region based on blast search.

A parser for CIGAR format alignments.

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

Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags

decoding the dbSNP bitfield containg detaild information

Parse publications for gene names in a fuzzy fashion

Interface for express beta diversity file formats

ruby parser for FastQC, a quality control software for high-throughput sequencing data.

a BioRuby plugin: handling genomic intervals,such as "chr1:123-456", and overlap state between two intervals

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

Ruby wrapper for the gff3-pltools.

A BioGem to submit jobs on a queue system

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."

Phylogenetic analysis using IQ-Tree via BioRuby