pRoloc

DOI: 10.18129/B9.bioc.pRoloc  

A unifying bioinformatics framework for spatial proteomics

Bioconductor version: Release (3.17)

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.

Author: Laurent Gatto, Oliver Crook and Lisa M. Breckels with contributions from Thomas Burger and Samuel Wieczorek

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("pRoloc")

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("pRoloc")

 

HTML	R Script	A transfer learning algorithm for spatial proteomics
HTML	R Script	Annotating spatial proteomics data
HTML	R Script	Bayesian spatial proteomics with pRoloc
HTML	R Script	Machine learning techniques available in pRoloc
HTML	R Script	Using pRoloc for spatial proteomics data analysis
PDF		Reference Manual
Text		NEWS
Video		pRoloc, pRolocdata and pRolocGUI

Details

biocViews	Classification, Clustering, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software
Version	1.40.1
In Bioconductor since	BioC 2.12 (R-3.0) (10.5 years)
License	GPL-2
Depends	R (>= 3.5), MSnbase(>= 1.19.20), MLInterfaces(>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel
Imports	stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics
LinkingTo	Rcpp, RcppArmadillo
Suggests	testthat, rmarkdown, pRolocdata(>= 1.9.4), roxygen2, xtable, rgl, BiocStyle(>= 2.5.19), hpar(>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick
SystemRequirements
Enhances
URL	https://github.com/lgatto/pRoloc
BugReports	https://github.com/lgatto/pRoloc/issues
Depends On Me	bandle, pRolocGUI
Imports Me
Suggests Me	MSnbase, pRolocdata, RforProteomics
Links To Me
Build Report

Package Archives

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

Source Package	pRoloc_1.40.1.tar.gz
Windows Binary	pRoloc_1.40.1.zip (64-bit only)
macOS Binary (x86_64)	pRoloc_1.40.1.tgz
macOS Binary (arm64)	pRoloc_1.40.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pRoloc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pRoloc
Bioc Package Browser	https://code.bioconductor.org/browse/pRoloc/
Package Short Url	https://bioconductor.org/packages/pRoloc/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive