rTANDEM: Interfaces the tandem protein identification algorithm in R

This package interfaces the tandem protein identification algorithm in R. Identification can be launched in the X!Tandem style, by using as sole parameter the path to a parameter file. But rTANDEM aslo provides extended syntax and functions to streamline launching analyses, as well as function to convert results, parameters and taxonomy to/from R. A related package, shinyTANDEM, provides visualization interface for result objects.

AuthorFrederic Fournier <frederic.fournier@crchuq.ulaval.ca>, Charles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>, Rene Paradis <rene.paradis@genome.ulaval.ca>, Arnaud Droit <arnaud.droit@crchuq.ulaval.ca>
Date of publicationNone
MaintainerFrederic Fournier <frederic.fournier@crchuq.ulaval.ca>
LicenseArtistic-1.0 | file LICENSE
Version1.14.0

View on Bioconductor

Functions

addTaxon Man page
AddTaxon Man page
getDegeneracy Man page
GetDegeneracy Man page
getParamFromXML Man page
GetParamFromXML Man page
getPeptides Man page
GetPeptides Man page
getProteins Man page
GetProteins Man page
getResultsFromXML Man page
GetResultsFromXML Man page
getTaxoFromXML Man page
GetTaxoFromXML Man page
ms2.plot Man page
print.rTParam Man page
rtandem Man page
rTANDEM Man page
rTANDEM-package Man page
rTParam Man page
rTResult-class Man page
rTResult_s-class Man page
rTTaxo Man page
setParamDefault Man page
SetParamDefault Man page
setParamIonTrap Man page
SetParamIonTrap Man page
setParamOrbitrap Man page
SetParamOrbitrap Man page
setParamPTMTreeSearch Man page
SetParamPTMTreeSearch Man page
setParamQuadTof05da Man page
SetParamQuadTof05da Man page
setParamQuadTof100ppm Man page
SetParamQuadTof100ppm Man page
setParamValue Man page
SetParamValue Man page
tandem Man page
writeParamToXML Man page
WriteParamToXML Man page
writeTaxoToXML Man page
WriteTaxoToXML Man page

Files

rTANDEM/DESCRIPTION
rTANDEM/LICENSE
rTANDEM/NAMESPACE
rTANDEM/NEWS
rTANDEM/R
rTANDEM/R/accessors.R rTANDEM/R/converters.R rTANDEM/R/parameters.R rTANDEM/R/rTANDEM.R rTANDEM/R/results.R rTANDEM/R/visualizers.R
rTANDEM/README
rTANDEM/build
rTANDEM/build/vignette.rds
rTANDEM/inst
rTANDEM/inst/doc
rTANDEM/inst/doc/rTANDEM.R
rTANDEM/inst/doc/rTANDEM.Rnw
rTANDEM/inst/doc/rTANDEM.pdf
rTANDEM/inst/extdata
rTANDEM/inst/extdata/default_input.xml
rTANDEM/inst/extdata/fasta
rTANDEM/inst/extdata/fasta/scd.fasta.pro
rTANDEM/inst/extdata/input.xml
rTANDEM/inst/extdata/ptmlist.txt
rTANDEM/inst/extdata/result.xml
rTANDEM/inst/extdata/tandem-input-style.xsl
rTANDEM/inst/extdata/tandem-style.css
rTANDEM/inst/extdata/tandem-style.xsl
rTANDEM/inst/extdata/taxonomy.xml
rTANDEM/inst/extdata/test_spectra.mgf
rTANDEM/man
rTANDEM/man/accessors.Rd rTANDEM/man/converters.Rd rTANDEM/man/parameters.Rd rTANDEM/man/rTANDEM-package.Rd rTANDEM/man/rTResult-class.Rd rTANDEM/man/tandem.Rd rTANDEM/man/visualizers.Rd
rTANDEM/src
rTANDEM/src/Makevars
rTANDEM/src/Makevars.in
rTANDEM/src/Makevars.win
rTANDEM/src/PTMTreeSearch.cpp
rTANDEM/src/PTMTreeSearch.h
rTANDEM/src/PTMTreeSearchScore.cpp
rTANDEM/src/PTMTreeSearchScore.h
rTANDEM/src/base64.cpp
rTANDEM/src/base64.h
rTANDEM/src/dataLoader.cpp
rTANDEM/src/dataLoader.h
rTANDEM/src/expat.h
rTANDEM/src/expat_external.h
rTANDEM/src/expat_external_old.h
rTANDEM/src/expat_old.h
rTANDEM/src/loadmspectrum.cpp
rTANDEM/src/loadmspectrum.h
rTANDEM/src/masscalc.cpp
rTANDEM/src/masscalc.h
rTANDEM/src/mbiomlreport.cpp
rTANDEM/src/mbiomlreport.h
rTANDEM/src/mcleave.h
rTANDEM/src/mdomains.h
rTANDEM/src/mhistogram.h
rTANDEM/src/mmotif.h
rTANDEM/src/mpam.cpp
rTANDEM/src/mpam.h
rTANDEM/src/mplugin.cpp
rTANDEM/src/mplugin.h
rTANDEM/src/mpmods.cpp
rTANDEM/src/mpmods.h
rTANDEM/src/mprocess.cpp
rTANDEM/src/mprocess.h
rTANDEM/src/mrefine.cpp
rTANDEM/src/mrefine.h
rTANDEM/src/mreport.cpp
rTANDEM/src/mreport.h
rTANDEM/src/mscore.cpp
rTANDEM/src/mscore.h
rTANDEM/src/mscore_hrk.cpp
rTANDEM/src/mscore_hrk.h
rTANDEM/src/mscore_k.cpp
rTANDEM/src/mscore_k.h
rTANDEM/src/mscore_tandem.cpp
rTANDEM/src/mscore_tandem.h
rTANDEM/src/mscorepam.h
rTANDEM/src/mscorestate.h
rTANDEM/src/msemistate.h
rTANDEM/src/msequence.h
rTANDEM/src/msequencecollection.cpp
rTANDEM/src/msequencecollection.h
rTANDEM/src/msequenceserver.cpp
rTANDEM/src/msequenceserver.h
rTANDEM/src/msequtilities.cpp
rTANDEM/src/msequtilities.h
rTANDEM/src/mspectrum.h
rTANDEM/src/mspectrumcondition.cpp
rTANDEM/src/mspectrumcondition.h
rTANDEM/src/mtermmods.cpp
rTANDEM/src/mtermmods.h
rTANDEM/src/mxxcleavage.cpp
rTANDEM/src/mxxcleavage.h
rTANDEM/src/resource.h
rTANDEM/src/saxbiomlhandler.cpp
rTANDEM/src/saxbiomlhandler.h
rTANDEM/src/saxgamlhandler.cpp
rTANDEM/src/saxgamlhandler.h
rTANDEM/src/saxhandler.cpp
rTANDEM/src/saxhandler.h
rTANDEM/src/saxmodhandler.cpp
rTANDEM/src/saxmodhandler.h
rTANDEM/src/saxmzdatahandler.cpp
rTANDEM/src/saxmzdatahandler.h
rTANDEM/src/saxmzmlhandler.cpp
rTANDEM/src/saxmzmlhandler.h
rTANDEM/src/saxmzxmlhandler.cpp
rTANDEM/src/saxmzxmlhandler.h
rTANDEM/src/saxsaphandler.cpp
rTANDEM/src/saxsaphandler.h
rTANDEM/src/saxtandeminputhandler.cpp
rTANDEM/src/saxtandeminputhandler.h
rTANDEM/src/saxtaxhandler.cpp
rTANDEM/src/saxtaxhandler.h
rTANDEM/src/stack_ptmtreesearch.h
rTANDEM/src/stdafx.cpp
rTANDEM/src/stdafx.h
rTANDEM/src/tandem.cpp
rTANDEM/src/tandem.h
rTANDEM/src/xmlparameter.cpp
rTANDEM/src/xmlparameter.h
rTANDEM/src/xmltaxonomy.cpp
rTANDEM/src/xmltaxonomy.h
rTANDEM/vignettes
rTANDEM/vignettes/rTANDEM.Rnw

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