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bioruby

bioruby

constants

Libraries of physical and chemical constants

dblinker

Code which generates allowable crosslinks from PDB files and can write those into PyMol.

diadem

Dynamic Isotope calculations

distribution

Statistical Distributions multi library wrapper. Uses Ruby by default and C (statistics2/GSL) or Java extensions where available.

double_disulfide_searcher

emass

A copy of Perttu Haimi's implementation of the Rockwood & Haimi 2006 JASMS "Efficient Calculation of Accurate Masses of Isotopic Peaks" method. Includes some fixes which are tracked via version control.

gene_ontology

simple class for working with GO (gene ontology); also see Bio::GO classes in bioruby

gnuplot-multiplot

enhances the gnuplot gem with multiplot capability

guimsconverter

This is a Ruby/Shoes based GUI for enabling those who dislike CLI programs to easily convert their RAW files to formats conducive to downstream processing.

isoelectric_calc

Calculates pI values for given protein sequences

katamari

mass spectrometry proteomics analysis pipeline based on KatamariDotei

katamaridotei

An MS proteomic analysis pipeline developed under Prince Labs (Still in development)

kder

A KDE implementation in ruby

lipid_classifier

Lipid classification tool

mascot-dat

A parser for Mascot DAT files

massifquant

Kalman tracker for binless quantification of chromatographic features in mass spectrometry proteomics

metfrag

Match Predicted Fragments with Mass Spectra

metriculator

Performance metric tool for LCMS and MS experiments.

ms-archiver

A package to archive and analyze MS data over both Windows and Linux machines and archive all the files to both a database and a network location.

ms-ident

mspire library for dealing with identifications from mass spectrometry

ms-isotoped

Code to find and identify isotopically labeled crosslinkers in Mass Spectrometry data.

ms-msconvert

Servers and wrappers offering a convenient interface to the ProteomeWizard (pwiz) msconvert utility

ms-qspecprep

This is a package that can prep files completely for a statistical comparison by the QSpec package

ms-quant

quantitation for mass spectrometry proteomics experiments. This project is not associated with MSQuant(http://msquant.sourceforge.net/), even though the goals are similar.

ms-quant-validator-misc

For validating various ms quantitation engines (fairly custom)

ms-testdata

Stores larger data files for commonly used file formats

mspire

mass spectrometry proteomics in ruby

mspire-centroider

centroid profile spectra

mspire-envelope_extractor

Extract isotope envelopes for protein turnover studies