binary dependency management for ruby gems

Context binding for functions evaluation

Binnacle Distributed Logging and Push Service. See http://binnacle.io

bins x, y data into discrete bins using constant time binning. Useful.

A gem for calculating probabilities modelled by the binomial theorem.

simple binary file parser.

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

Data mining and machine learning algorithms for JRuby

Tools to manipulate blat files from the command line. Uses the Bio::Blat object from BioRuby, but the parser has been modified to avoid reading the whole psl file, it yields just the current entry and it is up to the consumer to decide to store it or not." s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"

ools to work with fasta files, indexed with samtools. The initial releases depend on bio-samtools, but that will change

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

Bioinformatics. Aggregate FastQC (quality control for Next Generation Sequencing -NGS-) results from many different samples in a single web page, with charts and tables organized and simplified. The main goal is to speed up the communication process with colleagues (PIs, Biologists, BioInformaticians).

Basic wrapper for the Kallistio Mapper

Simple, under development Ruby solution for UCSC LiftOver tool

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

Tools to find similarity between pangenomes.

Methods for handling multiwell plate annotations, includes ranges and quadrants

Server for polymarker. To be used with cron

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 mutations.