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.

AuthorLaurent Gatto [aut], Sebastian Gibb [aut, cre]
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

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