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pRoloc

This is the development version of pRoloc; for the stable release version, see pRoloc.

A unifying bioinformatics framework for spatial proteomics


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

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")
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 HTML R Script
Reference Manual PDF
NEWS Text
pRoloc, pRolocdata and pRolocGUI Video

Details

biocViews Classification, Clustering, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software
Version 1.43.0
In Bioconductor since BioC 2.12 (R-3.0) (11 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
System Requirements
URL https://github.com/lgatto/pRoloc
Bug Reports https://github.com/lgatto/pRoloc/issues
See More
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
Linking To Rcpp, RcppArmadillo
Enhances
Depends On Me bandle, pRolocGUI
Imports Me
Suggests Me MSnbase, pRolocdata, RforProteomics
Links To Me
Build Report Build Report

Package Archives

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

Source Package pRoloc_1.43.0.tar.gz
Windows Binary pRoloc_1.43.0.zip
macOS Binary (x86_64) pRoloc_1.43.0.tgz
macOS Binary (arm64)
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