Pbase: Manipulating and exploring protein and proteomics data

A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Pbase")
AuthorLaurent Gatto [aut], Sebastian Gibb [aut, cre]
Bioconductor views DataImport DataRepresentation Infrastructure MassSpectrometry Proteomics Visualization
Date of publicationNone
MaintainerSebastian Gibb <mail@sebastiangibb.de>, Laurent Gatto <lg390@cam.ac.uk>
LicenseGPL-3
Version0.14.0
https://github.com/ComputationalProteomicsUnit/Pbase

View on Bioconductor

Functions

aa Man page
aa,Proteins-method Man page
acols Man page
addIdentificationData,Proteins,character-method Man page
addPeptideFragments Man page
addPeptideFragments,Proteins,character-method Man page
ametadata Man page
ametadata,Proteins-method Man page
avarLabels Man page
avarLabels,Proteins-method Man page
calculateHeavyLabels Man page
class:Proteins Man page
cleave,Proteins-method Man page
etrid2grl Man page
isCleaved Man page
isForward Man page
isReverse Man page
length,Proteins-method Man page
mapToGenome Man page
mapToGenome,ANY,ANY-method Man page
mapToGenome-methods Man page
mapToGenome,Proteins,GRangesList-method Man page
metadata<-,Proteins-method Man page
metadata,Proteins-method Man page
p Man page
pcols Man page
pfeatures Man page
pfeatures,Proteins-method Man page
pfilter Man page
pfilter,Proteins-method Man page
plotAsAnnotationTrack Man page
plotAsGeneRegionTrack Man page
plot,Proteins,missing-method Man page
pmapToGenome Man page
pmapToGenome,ANY,ANY-method Man page
pmapToGenome-methods Man page
pmapToGenome,Proteins,GRangesList-method Man page
pmetadata Man page
pmetadata,Proteins-method Man page
pms Man page
Pparams Man page
Pparams-class Man page
pranges Man page
pranges<- Man page
pranges<-,Proteins,CompressedIRangesList-method Man page
pranges,Proteins-method Man page
proteinCoding Man page
proteinCoding,GRangesList-method Man page
proteinCoding,GRanges-method Man page
proteinCoding-methods Man page
proteinCoverage Man page
Proteins Man page
[,Proteins,ANY,ANY,ANY-method Man page
[,Proteins,ANY,ANY-method Man page
[[,Proteins,ANY,ANY-method Man page
Proteins,character,missing-method Man page
Proteins-class Man page
Proteins,missing,character-method Man page
Proteins,missing,missing-method Man page
proteotypic Man page
pvarLabels Man page
pvarLabels,Proteins-method Man page
rmEmptyRanges Man page
seqnames,Proteins-method Man page
show,Pparams-method Man page
show,Proteins-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AAStringSet-functions.R R/AllClasses.R R/AllGenerics.R R/GRanges.R R/Proteins-functions.R R/Proteins-methods.R R/coordinate-mapping-methods.R R/environments.R R/fasta-functions.R R/heavylabels-functions.R R/onAttach.R R/params.R R/peptides-functions.R R/plotting.R R/utils.R R/vigfigs.R
build
build/vignette.rds
data
data/datalist
data/p.rda
data/pms.rda
inst
inst/doc
inst/doc/Pbase-data.R
inst/doc/Pbase-data.Rmd
inst/doc/Pbase-data.html
inst/doc/ensucsc.R
inst/doc/ensucsc.Rmd
inst/doc/ensucsc.html
inst/doc/mapping.R
inst/doc/mapping.Rmd
inst/doc/mapping.html
inst/extdata
inst/extdata/01_test_database.fasta
inst/extdata/04_test_database.fasta
inst/extdata/HUMAN_2015_02_selected.fasta
inst/extdata/Thermo_Hela_PRTC_selected.mgf.gz
inst/extdata/Thermo_Hela_PRTC_selected.mzid
inst/extdata/heavylabels_groundtruth.csv
inst/extdata/heavylabels_proteins_of_interest.fasta
inst/scripts
inst/scripts/makep.R
man
man/Pparams-class.Rd man/Proteins-class.Rd man/calculateHeavyLabels.Rd man/coordinate-mapping-methods.Rd man/etrid2grl.Rd man/isReverse.Rd man/p.Rd man/plotAsAnnotationTrack.Rd man/proteinCoding-methods.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/donttest_Proteins-class.R tests/testthat/test_AAStringSet-functions.R tests/testthat/test_Proteins-functions.R tests/testthat/test_Proteins-methods.R tests/testthat/test_fasta-functions.R tests/testthat/test_heavylabels-functions.R tests/testthat/test_peptides-functions.R tests/testthat/test_utils.R
vignettes
vignettes/Pbase-data.Rmd
vignettes/ensucsc.Rmd
vignettes/mapping.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.