Bioruby core plugins

BioRuby plugins with dependecies from external library or tools

Restriction Enzyme Dataset from REBASE in yaml form

decoding the dbSNP bitfield containg detaild information

a method to get the nucleotide sequence of translations done by the EMBOSS bioinformatics package program transeq.

This API provides a complete set of methods and classes to access the Ensembl database using Ruby programming language

Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins. Requires local install of the program, which is available from http://bioinf.wehi.edu.au/exportpred/

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

Identify causative mutations in a model genome from NGS reads using the NGM method.

Encode any message string into a DNA sequence

Hydropathy scale for BioRuby

Provide access to the IlluminaHumanAnnotations. Database comes form Bioconductor's package lumiHumanIDMapping

This is very scrappy at the moment, and will need to be seriously cleaned up. It does what I need it to do for now. I'll fix it up in the coming weeks. Promise :)

Running and parsing of the protein transmembrane domain predictor octopus

Pipeline to remove contaminations from EST libraries

Ruby tools and scripts for QTL mapping, part of the qtlHD project

Digests DNA based on restriction enzyme cut patterns

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...

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.

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