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.

AuthorAnton Pervukhin <apervukh@minet.uni-jena.de>, Steffen Neumann <sneumann@ipb-halle.de>
Date of publicationNone
MaintainerSteffen Neumann <sneumann@ipb-halle.de>
LicenseGPL-2
Version1.34.0
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

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

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