DOI: 10.18129/B9.bioc.Pbase    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of Pbase; to use it, please install the devel version of Bioconductor.

Manipulating and exploring protein and proteomics data

Bioconductor version: Development (3.10)

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

Author: Laurent Gatto [aut, cre], Johannes Rainer [aut], Sebastian Gibb [aut]

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>

Citation (from within R, enter citation("Pbase")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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biocViews DataImport, DataRepresentation, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software, Visualization
Version 0.25.1
In Bioconductor since BioC 3.1 (R-3.2) (4.5 years)
License GPL-3
Depends R (>= 2.10), methods, BiocGenerics, Rcpp, Gviz
Imports cleaver(>= 1.3.6), Biobase, Biostrings(>= 2.47.5), IRanges(>= 2.13.11), S4Vectors(>= 0.17.24), mzID, mzR(>= 1.99.1), MSnbase(>= 1.15.5), Pviz, biomaRt, GenomicRanges(>= 1.31.7), rtracklayer(>= 1.39.6), ensembldb(>= 1.99.13), BiocParallel, AnnotationFilter
Suggests testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr, rmarkdown, BiocStyle, EnsDb.Hsapiens.v86(>= 2.0.0)
URL https://github.com/ComputationalProteomicsUnit/Pbase
BugReports https://github.com/ComputationalProteomicsUnit/Pbase/issues
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Source Package Pbase_0.25.1.tar.gz
Windows Binary Pbase_0.25.1.zip
Mac OS X 10.11 (El Capitan) Pbase_0.25.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/Pbase
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Pbase
Package Short Url https://bioconductor.org/packages/Pbase/
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