Pbase

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see Pbase.

Manipulating and exploring protein and proteomics data

DOI: 10.18129/B9.bioc.Pbase

Bioconductor version: 3.7

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]

Maintainer: Sebastian Gibb <mail at sebastiangibb.de>, Laurent Gatto <lg390 at cam.ac.uk>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("Pbase")

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

Documentation

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

browseVignettes("Pbase")

Pbase data HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, Infrastructure, MassSpectrometry, Proteomics, Software, Visualization

Version 0.20.0

In Bioconductor since BioC 3.1 (R-3.2) (9 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

System Requirements

URL https://github.com/ComputationalProteomicsUnit/Pbase

Bug Reports https://github.com/ComputationalProteomicsUnit/Pbase/issues

Suggests testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr, rmarkdown, BiocStyle, EnsDb.Hsapiens.v86(>= 2.0.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Pbase_0.20.0.tar.gz

Windows Binary Pbase_0.20.0.zip

Mac OS X 10.11 (El Capitan) Pbase_0.20.0.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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Old Source Packages for BioC 3.7 Source Archive