Rdisop: Decomposition of Isotopic Patterns

Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rdisop")
AuthorAnton Pervukhin <apervukh@minet.uni-jena.de>, Steffen Neumann <sneumann@ipb-halle.de>
Bioconductor views MassSpectrometry Metabolomics
Date of publicationNone
MaintainerSteffen Neumann <sneumann@ipb-halle.de>
LicenseGPL-2
Version1.36.0
https://github.com/sneumann/Rdisop

View on Bioconductor

Functions

addMolecules Man page
decomposeIsotopes Man page
decomposeMass Man page
getFormula Man page
getIsotope Man page
getMass Man page
getMolecule Man page
getScore Man page
getValid Man page
initializeCharges Man page
initializeCHNOPS Man page
initializeCHNOPSMgKCaFe Man page
initializeCHNOPSNaK Man page
initializeElements Man page
initializePSE Man page
isotopeScore Man page
subMolecules Man page

Files

ChangeLog
DESCRIPTION
INSTALL
NAMESPACE
R
R/Rdisop.R R/elements.R R/zzz.R
RcppSrc
build
build/vignette.rds
cleanup
inst
inst/CITATION
inst/doc
inst/doc/Rdisop.Rnw
inst/doc/Rdisop.pdf
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/runit.addsub.R
inst/unitTests/runit.charges.R-disabled
inst/unitTests/runit.keggexamples.R inst/unitTests/runit.limits.R inst/unitTests/runit.monoisotopic.R
man
man/addMolecules.Rd man/decomposeMass.Rd man/getMolecule.Rd man/initializeCHNOPS.Rd
src
src/Makevars
src/Makevars.win
src/disop.cpp
src/imslib
src/imslib/CMakeLists.txt
src/imslib/CODING
src/imslib/Doxyfile
src/imslib/Makefile
src/imslib/Makefile.am
src/imslib/Makefile.in
src/imslib/README
src/imslib/TODO
src/imslib/acinclude.m4
src/imslib/aclocal.m4
src/imslib/autogen.sh
src/imslib/cmake
src/imslib/cmake/FindCppUnit.cmake
src/imslib/config
src/imslib/config.h
src/imslib/config.h.cmake
src/imslib/config.h.in
src/imslib/config.log
src/imslib/config.status
src/imslib/config/config.guess
src/imslib/config/config.sub
src/imslib/config/depcomp
src/imslib/config/install-sh
src/imslib/config/ltmain.sh
src/imslib/config/missing
src/imslib/config/mkinstalldirs
src/imslib/configure
src/imslib/configure.ac
src/imslib/doc
src/imslib/doc/imslib-doc.h
src/imslib/doc/imslib.css
src/imslib/examples
src/imslib/examples/peaklist.cpp
src/imslib/examples/stopwatch.cpp
src/imslib/imslib.ebuild
src/imslib/install-gentoo
src/imslib/install-official
src/imslib/libims.pc
src/imslib/libims.pc.cmake
src/imslib/libims.pc.in
src/imslib/libtool
src/imslib/libtool64
src/imslib/math.h.cmake
src/imslib/res
src/imslib/res/amino-acid-average.masses-frequencies
src/imslib/res/amino-acid-mono.masses-frequencies
src/imslib/res/atom-average.masses
src/imslib/res/atom-mono.masses
src/imslib/res/dna-average.masses
src/imslib/res/dna-mono.masses
src/imslib/src
src/imslib/src/CMakeLists.txt
src/imslib/src/ims
src/imslib/src/ims/alphabet.cpp
src/imslib/src/ims/alphabet.h
src/imslib/src/ims/base
src/imslib/src/ims/base/exception
src/imslib/src/ims/base/exception/exception.h
src/imslib/src/ims/base/exception/invalidargumentexception.h
src/imslib/src/ims/base/exception/ioexception.h
src/imslib/src/ims/base/exception/unknowncharacterexception.h
src/imslib/src/ims/base/parser
src/imslib/src/ims/base/parser/abstractmoleculesequenceparser.h
src/imslib/src/ims/base/parser/alphabetparser.h
src/imslib/src/ims/base/parser/alphabettextparser.cpp
src/imslib/src/ims/base/parser/alphabettextparser.h
src/imslib/src/ims/base/parser/distributedalphabetparser.h
src/imslib/src/ims/base/parser/distributedalphabettextparser.cpp
src/imslib/src/ims/base/parser/distributedalphabettextparser.h
src/imslib/src/ims/base/parser/keggligandcompoundsparser.cpp
src/imslib/src/ims/base/parser/keggligandcompoundsparser.h
src/imslib/src/ims/base/parser/massesparser.h
src/imslib/src/ims/base/parser/massestextparser.cpp
src/imslib/src/ims/base/parser/massestextparser.h
src/imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp
src/imslib/src/ims/base/parser/moleculeionchargemodificationparser.h
src/imslib/src/ims/base/parser/moleculesequenceparser.cpp
src/imslib/src/ims/base/parser/moleculesequenceparser.h
src/imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp
src/imslib/src/ims/base/parser/standardmoleculesequenceparser.h
src/imslib/src/ims/calib
src/imslib/src/ims/calib/calibrator.h
src/imslib/src/ims/calib/geometriccalibrator.h
src/imslib/src/ims/calib/linearpointsetmatcher.cpp
src/imslib/src/ims/calib/linearpointsetmatcher.h
src/imslib/src/ims/calib/linepairstabber.cpp
src/imslib/src/ims/calib/linepairstabber.h
src/imslib/src/ims/calib/linestabbingcalibrator.h
src/imslib/src/ims/calib/lmsregressioncalibrator.h
src/imslib/src/ims/calib/matchmatrix.cpp
src/imslib/src/ims/calib/matchmatrix.h
src/imslib/src/ims/calib/pointsetmatchercalibrator.h
src/imslib/src/ims/characteralphabet.cpp
src/imslib/src/ims/characteralphabet.h
src/imslib/src/ims/chebyshevfitter.h
src/imslib/src/ims/composedelement.cpp
src/imslib/src/ims/composedelement.h
src/imslib/src/ims/decomp
src/imslib/src/ims/decomp/classicaldpmassdecomposer.h
src/imslib/src/ims/decomp/decomputils.h
src/imslib/src/ims/decomp/fastintegermassdecomposer.h
src/imslib/src/ims/decomp/integermassdecomposer.h
src/imslib/src/ims/decomp/massdecomposer.h
src/imslib/src/ims/decomp/realmassdecomposer.cpp
src/imslib/src/ims/decomp/realmassdecomposer.h
src/imslib/src/ims/decomp/residuetable.h
src/imslib/src/ims/decomp/twomassdecomposer.h
src/imslib/src/ims/decomp/twomassdecomposer2.h
src/imslib/src/ims/distributedalphabet.cpp
src/imslib/src/ims/distributedalphabet.h
src/imslib/src/ims/distributeddata.h
src/imslib/src/ims/distributionprobabilityscorer.cpp
src/imslib/src/ims/distributionprobabilityscorer.h
src/imslib/src/ims/element.cpp
src/imslib/src/ims/element.h
src/imslib/src/ims/elementsortcriteria.h
src/imslib/src/ims/fragmenter.h
src/imslib/src/ims/fragmentpeak.h
src/imslib/src/ims/functors
src/imslib/src/ims/functors/alphabetgetmass.h
src/imslib/src/ims/idsequence.h
src/imslib/src/ims/intensitypeak.h
src/imslib/src/ims/isotopedistribution.cpp
src/imslib/src/ims/isotopedistribution.h
src/imslib/src/ims/isotopespecies.cpp
src/imslib/src/ims/isotopespecies.h
src/imslib/src/ims/logger.h
src/imslib/src/ims/markovsequencegenerator.h
src/imslib/src/ims/massintensitypeak.h
src/imslib/src/ims/massintensitytofpeak.h
src/imslib/src/ims/masspeak.h
src/imslib/src/ims/masstofpeak.h
src/imslib/src/ims/modifier
src/imslib/src/ims/modifier/intensitynormalizermodifier.h
src/imslib/src/ims/modifier/massrangemodifier.h
src/imslib/src/ims/modifier/modifier.h
src/imslib/src/ims/modifier/multimodifier.h
src/imslib/src/ims/modifier/noisemodifier.h
src/imslib/src/ims/modifier/shiftmodifier.h
src/imslib/src/ims/modifier/sortmodifier.h
src/imslib/src/ims/modifier/unificationmodifier.h
src/imslib/src/ims/modifier/voidmodifier.h
src/imslib/src/ims/nitrogenrulefilter.cpp
src/imslib/src/ims/nitrogenrulefilter.h
src/imslib/src/ims/peakcompare.h
src/imslib/src/ims/peakequalby.h
src/imslib/src/ims/peakequalto.h
src/imslib/src/ims/peaklist.h
src/imslib/src/ims/peakpropertyiterator.h
src/imslib/src/ims/pmffragmenter.h
src/imslib/src/ims/randomsequencegenerator.h
src/imslib/src/ims/sequencegenerator.h
src/imslib/src/ims/tandemfragmenter.h
src/imslib/src/ims/tclap
src/imslib/src/ims/tclap/Arg.h
src/imslib/src/ims/tclap/ArgException.h
src/imslib/src/ims/tclap/CmdLine.h
src/imslib/src/ims/tclap/CmdLineInterface.h
src/imslib/src/ims/tclap/CmdLineOutput.h
src/imslib/src/ims/tclap/DocBookOutput.h
src/imslib/src/ims/tclap/HelpVisitor.h
src/imslib/src/ims/tclap/IgnoreRestVisitor.h
src/imslib/src/ims/tclap/MultiArg.h
src/imslib/src/ims/tclap/StdOutput.h
src/imslib/src/ims/tclap/SwitchArg.h
src/imslib/src/ims/tclap/UnlabeledMultiArg.h
src/imslib/src/ims/tclap/UnlabeledValueArg.h
src/imslib/src/ims/tclap/ValueArg.h
src/imslib/src/ims/tclap/VersionVisitor.h
src/imslib/src/ims/tclap/Visitor.h
src/imslib/src/ims/tclap/XorHandler.h
src/imslib/src/ims/tofpeak.h
src/imslib/src/ims/transformation.cpp
src/imslib/src/ims/transformation.h
src/imslib/src/ims/utils
src/imslib/src/ims/utils/compose_f_gx_hy_t.h
src/imslib/src/ims/utils/compose_f_gx_t.h
src/imslib/src/ims/utils/distribution.cpp
src/imslib/src/ims/utils/distribution.h
src/imslib/src/ims/utils/gcd.h
src/imslib/src/ims/utils/math.h
src/imslib/src/ims/utils/matrix.h
src/imslib/src/ims/utils/print.h
src/imslib/src/ims/utils/stopwatch.h
src/imslib/src/ims/weights.cpp
src/imslib/src/ims/weights.h
src/imslib/stamp-h1
src/imslib/tests
src/imslib/tests/alphabettest.cpp
src/imslib/tests/base
src/imslib/tests/base/parser
src/imslib/tests/base/parser/massestextparsertest.cpp
src/imslib/tests/base/parser/moleculesequenceparsertest.cpp
src/imslib/tests/calib
src/imslib/tests/calib/linearpointsetmatchertest.cpp
src/imslib/tests/calib/linepairstabbertest.cpp
src/imslib/tests/calib/matchmatrixtest.cpp
src/imslib/tests/chebyshevfittertest.cpp
src/imslib/tests/composedelementtest.cpp
src/imslib/tests/decomp
src/imslib/tests/decomp/integermassdecomposertest.cpp
src/imslib/tests/decomp/realmassdecomposertest.cpp
src/imslib/tests/decomp/twomassdecomposer2test.cpp
src/imslib/tests/distributedalphabettest.cpp
src/imslib/tests/distributionprobabilityscorertest.cpp
src/imslib/tests/elementtest.cpp
src/imslib/tests/exceptiontest.cpp
src/imslib/tests/fragmentpeaktest.cpp
src/imslib/tests/identitytransformationtest.cpp
src/imslib/tests/intensitypeaktest.cpp
src/imslib/tests/isotopedistributiontest.cpp
src/imslib/tests/isotopespeciestest.cpp
src/imslib/tests/lineartransformationtest.cpp
src/imslib/tests/markovsequencegeneratortest.cpp
src/imslib/tests/massintensitypeaktest.cpp
src/imslib/tests/massintensitytofpeaktest.cpp
src/imslib/tests/masspeaktest.cpp
src/imslib/tests/masstofpeaktest.cpp
src/imslib/tests/modifier
src/imslib/tests/modifier/intensitynormalizermodifiertest.cpp
src/imslib/tests/modifier/massrangemodifiertest.cpp
src/imslib/tests/modifier/multimodifiertest.cpp
src/imslib/tests/modifier/noisemodifiertest.cpp
src/imslib/tests/modifier/shiftmodifiertest.cpp
src/imslib/tests/modifier/sortmodifiertest.cpp
src/imslib/tests/modifier/unificationmodifiertest.cpp
src/imslib/tests/modifier/voidmodifiertest.cpp
src/imslib/tests/peaklisttest.cpp
src/imslib/tests/peakpropertyiteratortest.cpp
src/imslib/tests/pmffragmentertest.cpp
src/imslib/tests/polynomialtransformationtest.cpp
src/imslib/tests/randomsequencegeneratortest.cpp
src/imslib/tests/roundtest.cpp
src/imslib/tests/shifttransformationtest.cpp
src/imslib/tests/stopwatchtest.cpp
src/imslib/tests/tests.cpp
src/imslib/tests/tofpeaktest.cpp
src/imslib/tests/utils
src/imslib/tests/utils/log4cpp
src/imslib/tests/utils/log4cpp/log4cppappendertest.cpp
src/imslib/tests/utils/log4cpp/log4cppcategorytest.cpp
src/imslib/tests/weightstest.cpp
src/imslib/tools
src/imslib/tools/CMakeLists.txt
src/imslib/tools/decompcommandline.h
src/imslib/tools/decompvalidation.cpp
src/imslib/tools/eispectraanalysis.cpp
src/imslib/tools/elementalcompositions.cpp
src/imslib/tools/histogram.cpp
src/imslib/tools/imsdecomp.cpp
src/imslib/tools/imsfrag.cpp
src/imslib/tools/imsintdecomp.cpp
src/imslib/tools/keggruntimes.cpp
src/imslib/tools/numberdecompositions.cpp
src/imslib/tools/options.cpp
src/imslib/tools/options.h
src/imslib/tools/peaklistvalidation.cpp
src/imslib/tools/scoredecompositions.cpp
tests
tests/doRUnit.R
vignettes
vignettes/Make.file
vignettes/Rdisop.Rnw
vignettes/Rdisop.bib

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