proteoQC: An R package for proteomics data quality control

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This package creates a HTML format QC report for MS/MS-based proteomics data. The report is intended to allow the user to quickly assess the quality of proteomics data.

Author
Bo Wen <wenbo@genomics.cn>, Laurent Gatto <lg390@cam.ac.uk>
Date of publication
None
Maintainer
Bo Wen <wenbo@genomics.cn>
License
LGPL-2
Version
1.10.0

View on Bioconductor

Man pages

addSummaryChart
Add PRIDE summary charts
calcMSQCMetrics
Calculate the MS1 and MS2 level QC metrics
chargeStat
Charge distribution
cntStat
contaminants stat
combineRun
Combine multiple results
createTargetDecoyDB
Create target-decoy database
getEnzyme
Get the enzymes list
getMods
Get the modification list
labelRatio
Calculate the labeling efficiency of isobaric labeling data
loadmsQCres
Load the result of 'msQCpipe'
msQCpipe
The main function of msQC pipeline
plotBioRepVenn
Venn plot in biological replicate level
plotFractionIDResult
Barplot in different level for each fraction
plotMS1Error
plot MS1 mass error
plotMS2Error
plot MS2 mass error
plotMS2Error_obsolete
plot MS2 mass error
plotSampleIDResultErrorBar
Error barplot in different level for each fraction
plotSampleVenn
Venn plot in sample level
plotTechRepVenn
Venn plot in technical replicate level
print.msQCres
Print the information of msQCres object
proteinGroup
Protein inference
reportHTML
HTML format report generator
runTandem
Run X!Tandem
showEnzyme
Shown all enzymes
showMods
Shown all modifications

Files in this package

proteoQC/DESCRIPTION
proteoQC/NAMESPACE
proteoQC/NEWS
proteoQC/R
proteoQC/R/ms12QC.R
proteoQC/R/msQC.R
proteoQC/R/report.R
proteoQC/R/tools.R
proteoQC/R/visualization.R
proteoQC/build
proteoQC/build/vignette.rds
proteoQC/inst
proteoQC/inst/config
proteoQC/inst/config/enzyme.txt
proteoQC/inst/config/mods.txt
proteoQC/inst/db
proteoQC/inst/db/crap.fasta
proteoQC/inst/db/crap.txt
proteoQC/inst/doc
proteoQC/inst/doc/proteoQC.R
proteoQC/inst/doc/proteoQC.Rnw
proteoQC/inst/doc/proteoQC.pdf
proteoQC/inst/extdata
proteoQC/inst/extdata/PXD000864-design.txt
proteoQC/inst/extdata/mgf.zip
proteoQC/inst/extdata/pep.zip
proteoQC/inst/extdata/qc.zip
proteoQC/inst/scripts
proteoQC/inst/scripts/make_big_qc.R
proteoQC/inst/scripts/skim.r
proteoQC/inst/tool
proteoQC/inst/tool/tandemparser.jar
proteoQC/inst/unitTests
proteoQC/inst/unitTests/test_loadmsQCres.R
proteoQC/man
proteoQC/man/addSummaryChart.Rd
proteoQC/man/calcMSQCMetrics.Rd
proteoQC/man/chargeStat.Rd
proteoQC/man/cntStat.Rd
proteoQC/man/combineRun.Rd
proteoQC/man/createTargetDecoyDB.Rd
proteoQC/man/getEnzyme.Rd
proteoQC/man/getMods.Rd
proteoQC/man/labelRatio.Rd
proteoQC/man/loadmsQCres.Rd
proteoQC/man/msQCpipe.Rd
proteoQC/man/plotBioRepVenn.Rd
proteoQC/man/plotFractionIDResult.Rd
proteoQC/man/plotMS1Error.Rd
proteoQC/man/plotMS2Error.Rd
proteoQC/man/plotMS2Error_obsolete.Rd
proteoQC/man/plotSampleIDResultErrorBar.Rd
proteoQC/man/plotSampleVenn.Rd
proteoQC/man/plotTechRepVenn.Rd
proteoQC/man/print.msQCres.Rd
proteoQC/man/proteinGroup.Rd
proteoQC/man/reportHTML.Rd
proteoQC/man/runTandem.Rd
proteoQC/man/showEnzyme.Rd
proteoQC/man/showMods.Rd
proteoQC/src
proteoQC/src/utilities.cpp
proteoQC/tests
proteoQC/tests/runTests.R
proteoQC/vignettes
proteoQC/vignettes/proteoQC.Rnw
proteoQC/vignettes/proteoQC.bib