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

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 :)

Simple, under development Ruby solution for UCSC LiftOver tool

Log4r wrapper for BioRuby

Client package for creating, sending, recieving and consuming SOAP messages from BioModels search engine

Help for working with the output of the .delta files produced by nucmer and promer

Tools to find similarity between pangenomes.

Pipeline to remove contaminations from EST libraries

Iterate through a samtools pileup file

The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptides in Plasmodium falciparum. This is an implementation of that algorithm.

Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat

Server for polymarker. To be used with cron

Just a test

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

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...

A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA metadata) SQLite database.

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.