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 package is for version 3.10 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
Bioconductor version: 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("Pbase")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software, Visualization |
| Version | 0.26.0 |
| 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 |
See More
| Suggests | testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr, rmarkdown, BiocStyle, EnsDb.Hsapiens.v86(>= 2.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Pbase_0.26.0.tar.gz |
| Windows Binary | Pbase_0.26.0.zip |
| Mac OS X 10.11 (El Capitan) | Pbase_0.26.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |