pRoloc

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see pRoloc.

A unifying bioinformatics framework for spatial proteomics

Bioconductor version: 3.14

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 "4.1") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Clustering, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software

Version 1.34.0

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

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

Linking To Rcpp, RcppArmadillo

Enhances

Depends On Me pRolocGUI, proteomics

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_1.34.0.tar.gz

Windows Binary pRoloc_1.34.0.zip

macOS 10.13 (High Sierra) pRoloc_1.34.0.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 3.14 Source Archive