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.

Author
Frederic 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 publication
None
Maintainer
Frederic Fournier <frederic.fournier@crchuq.ulaval.ca>
License
Artistic-1.0 | file LICENSE
Version
1.14.0

View on Bioconductor

Man pages

accessors
Extract information from rTANDEM result object
converters
Converts X!Tandem xml files to R objects and vice versa
parameters
Creates and manipulates parameter objects for rTANDEM
rTANDEM-package
An R encapsulation of X!TANDEM ('Jackhammer' release,...
rTResult-class
Class "rTResult" and "rTResult_s"
tandem
Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R...
visualizers
Plot spectrum from a rTResult object

Files in this package

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