Alexandre Masselot > InSilicoSpectro-1.3.24

InSilicoSpectro-1.3.24

This Release InSilicoSpectro-1.3.24  [Download] [Browse 20 Aug 2008
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License lgpl
Special Files
Makefile.PL
META.yml
README

Modules

CGIUtils      
DefEnv     0.9
InSilicoSpectro Open source Perl library for proteomics     1.3.24
InSilicoSpectro::InSilico::AASequence Elementary protein sequence.      
InSilicoSpectro::InSilico::CleavEnzyme Basic enzyme object.      
InSilicoSpectro::InSilico::ExpCalibrator Calibrates a RetentionTimer predictor based on experimental data      
InSilicoSpectro::InSilico::InternIonSeries Perl class to represent internal fragment ion series.      
InSilicoSpectro::InSilico::IonSeries Perl class to represent fragment ion series.      
InSilicoSpectro::InSilico::IsoelPoint A class for peptide isoelectric point (pI) prediction      
InSilicoSpectro::InSilico::MSMSOutput An object implementing common display/output methods for masses      
InSilicoSpectro::InSilico::MSMSTheoSpectrum Perl class to represent MS/MS theoretical spectra      
InSilicoSpectro::InSilico::MassCalculator Implements common mass computations in mass spectrometry      
InSilicoSpectro::InSilico::ModRes Residue modifications package      
InSilicoSpectro::InSilico::PMFMatch Perl class to represent PMF matches      
InSilicoSpectro::InSilico::Peptide A class for digestion products      
InSilicoSpectro::InSilico::RetentionTimer A base class for implementing a peptide retention time predictor      
InSilicoSpectro::InSilico::RetentionTimer::Hodges Prediction of peptide retention time method by sum of amino acid coefficients.      
InSilicoSpectro::InSilico::RetentionTimer::Petritis Prediction of peptide retention time by neural network training      
InSilicoSpectro::InSilico::Sequence Elementary sequence object      
InSilicoSpectro::InSilico::TermIonSeries Perl class to represent N-/C-terminal fragment ion series.      
InSilicoSpectro::Spectra::ExpSpectrum A class for representing spectra.      
InSilicoSpectro::Spectra::Filter::MSFilter     0.9
InSilicoSpectro::Spectra::Filter::MSFilterAlgorithm     0.9
InSilicoSpectro::Spectra::Filter::MSFilterCollection     0.9
InSilicoSpectro::Spectra::Filter::MSFilterDirectValue     0.9
InSilicoSpectro::Spectra::MSMSCmpd      
InSilicoSpectro::Spectra::MSMSSpectra      
InSilicoSpectro::Spectra::MSRun      
InSilicoSpectro::Spectra::MSSpectra      
InSilicoSpectro::Spectra::PeakDescriptor Description of peak properties      
InSilicoSpectro::Spectra::PhenyxPeakDescriptor      
InSilicoSpectro::Utils::FileCached      
InSilicoSpectro::Utils::Files      
InSilicoSpectro::Utils::XML::SaxIndexMaker      
InSilicoSpectro::Utils::io      

Documentation

InSilico Build.PL  
InSilicoSpectro::InSilico  
InSilicoSpectro::Spectra  
InSilicoSpectro::Utils  
MSMSTheoSPectrum Perl class to represent MS/MS theoretical spectra  
cgi/cgiInSilicoDef.pl  
cgi/showEnv.pl  
cgiComputePI.pl  
cgiComputeRT.pl  
cgiConvertSpectra.pl  
computePI.pl Compute isoelectric point (pI)  
computeRT.pl Compute retention time  
convertSpectra.pl  
extractUniquePeptSpectra.pl Extracts unique peptides from a .peptSpectra.xml file  
filterPeptSpectra.pl Filters the matches of a .peptSpectra.xml file  
fragErrorDistr.pl Extraction of fragment ion mass errors from .peptSpectra.xml files  
getIonIntensities.pl Extraction of ion intensities information from a .peptSpectra.xml file  
idr2pept.pl Extraction of reliable peptide/spectrum matches from Phenyx .idr.xml files  
importResid.pl  
indexXml.pl  
mascot2pept.pl Extraction of reliable peptide/spectrum matches from Mascot .dat files  
parentErrorDistr.pl Extraction of parent ion mass errors from .peptSpectra.xml files  
splice-idj.pl extract a subset of spectra from an idj to porduce another one  
split-mgf.pl  
splitPeptSpectraAtRandom.pl Splits a .peptSpectra.xml file in two .peptSpectra.xml files