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

Digests DNA based on restriction enzyme cut patterns

An MCP server that provides access to BioRuby KEGG functionality, allowing AI assistants to query KEGG databases for biological pathways, compounds, and other molecular information.

Provides PhyloXML support for BioRuby. This bioruby-phyloxml gem replaces old unmaintained bio-phyloxml gem.

New Sambamba library comes with a command-line tool for working with SAM/BAM files. This gem brings some of its functionality to Ruby.

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

Wrapper of samtools for ruby. This project was born from the need to add support of BAM files to the gee_fu genome browser (http://github.com/danmaclean/gee_fu).

Entries in a flatfile will be parased by the BioRuby's Bio::FlatFile.auto module. These entries are used as queries for the Sun Grid Engine (SGE) system. Huge amount of queries are automatically splitted into subdirectories. With a specified command line to be executed, queries are submited to th...

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

Takes a GFF and genomic sequence file, constructs CDS and when given a position and alternative base will report whether this change is in a coding region and if it results in a synonymous or non-synonymous mutation.

A bioruby plugin for interaction with the transmembrane predictor TMHMM

BioRuby plugin for UniChem REST Web service

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

Bindings to some internals of the velvet assembler.

Enables the localisation predictor WoLF PSORT to be run locally. The algorithm is available at http://wolfpsort.org/

a library and commandline tool to pick causative mutation from bulks segregant sequencing