Pbase: Manipulating and exploring protein and proteomics data

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

Author
Laurent Gatto [aut], Sebastian Gibb [aut, cre]
Date of publication
None
Maintainer
Sebastian Gibb <mail@sebastiangibb.de>, Laurent Gatto <lg390@cam.ac.uk>
License
GPL-3
Version
0.14.0
URLs

View on Bioconductor

Man pages

calculateHeavyLabels
Calculate heavy labeled peptides
coordinate-mapping-methods
Map range coordinates between proteins and genome space
etrid2grl
From a transcript identifier to 'GRanges' object
isReverse
Are all the ranges on the same strand
p
Data accompanying the 'Pbase' package
plotAsAnnotationTrack
Plot gene region and annotation tracks
Pparams-class
Class '"Pparams"'
proteinCoding-methods
Only keep protein coding ranges
Proteins-class
The 'Proteins' Class for Proteomics Data And Meta-Data

Files in this package

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