Pbase

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")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML R Script Pbase data
PDF   Reference Manual
Text   NEWS

Details

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
LinkingTo
Suggests testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr, rmarkdown, BiocStyle, EnsDb.Hsapiens.v86(>= 2.0.0)
SystemRequirements
Enhances
URL https://github.com/ComputationalProteomicsUnit/Pbase
BugReports https://github.com/ComputationalProteomicsUnit/Pbase/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

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/
Package Downloads Report Download Stats

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