InSilicoSpectro

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InSilicoSpectro-1.3.24

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20 Aug 2008

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License

LGPL

Special Files

META.yml

Makefile.PL

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