pRoloc

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12

A unifying bioinformatics framework for spatial proteomics

Bioconductor version: Development (3.24)

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 [aut], Lisa Breckels [aut, cre], Thomas Burger [ctb], Samuel Wieczorek [ctb], Charlotte Hutchings [ctb], Oliver Crook [aut]

Maintainer: Lisa Breckels <lms79 at cam.ac.uk>

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

Laurent Gatto, Lisa Breckels, Oliver Crook. pRoloc: A unifying bioinformatics framework for spatial proteomics. doi:10.18129/B9.bioc.pRoloc, R package version 1.53.0, https://bioconductor.org/packages/pRoloc.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software
Version	1.53.0
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 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, colorspace
System Requirements
URL	https://github.com/lgatto/pRoloc
Bug Reports	https://github.com/lgatto/pRoloc/issues

Suggests	testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick, umap
Linking To	Rcpp, RcppArmadillo
Enhances
Depends On Me	bandle, pRolocGUI
Imports Me
Suggests Me	MSnbase, pRolocdata, RforProteomics
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	pRoloc_1.53.0.tar.gz
Windows Binary (x86_64)	pRoloc_1.53.0.zip
macOS Binary (big-sur-x86_64)	pRoloc_1.53.0.tgz
macOS Binary (sonoma-arm64)	pRoloc_1.53.0.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