Ripper of binary files

Gem for easy writing and executing scripts in Rails Application. For my purposes much better than Rake, Thor and Rails Runner.

Pure ruby implementation of binary search for Ruby arrays and similiar data structures. Supports ascending and descending sort order, searching for exact and nearest matches, and has a versatile API. Uses linear search for small arrays to make use of the internal cache of moden CPUs.

Binary stream processor

OpenObject xmlrpc interface

Bintray API Client

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 useful in other contexts as well.

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.