pRoloc

DOI: 10.18129/B9.bioc.pRoloc    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see pRoloc.

A unifying bioinformatics framework for spatial proteomics

Bioconductor version: 3.15

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 "4.2") 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 1.36.0
In Bioconductor since BioC 2.12 (R-3.0) (9.5 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(>= 1.15.3), 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, proteomics
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_1.36.0.tar.gz
Windows Binary pRoloc_1.36.0.zip
macOS Binary (x86_64) pRoloc_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pRoloc
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pRoloc
Package Short Url https://bioconductor.org/packages/pRoloc/
Package Downloads Report Download Stats

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