pRoloc

DOI: 10.18129/B9.bioc.pRoloc    

A unifying bioinformatics framework for spatial proteomics

Bioconductor version: Release (3.6)

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 and Lisa M. Breckels with contributions from Thomas Burger and Samuel Wieczorek

Maintainer: Laurent Gatto <lg390 at cam.ac.uk>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pRoloc")

Documentation

HTML	R Script	A transfer learning algorithm for spatial proteomics
HTML	R Script	Annotating spatial proteomics data
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, MassSpectrometry, Proteomics, QualityControl, Software
Version	1.18.0
In Bioconductor since	BioC 2.12 (R-3.0) (5 years)
License	GPL-2
Depends	R (>= 2.15), MSnbase(>= 1.19.20), MLInterfaces(>= 1.37.1), methods, Rcpp (>= 0.10.3), BiocParallel
Imports	Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, Rtsne (>= 0.13), lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics
LinkingTo	Rcpp, RcppArmadillo
Suggests	testthat, rmarkdown, pRolocdata(>= 1.9.4), roxygen2, synapter, xtable, rgl, BiocStyle(>= 2.5.19), hpar(>= 1.15.3), dplyr, GO.db, AnnotationDbi
SystemRequirements
Enhances
URL	https://github.com/lgatto/pRoloc
BugReports	https://github.com/lgatto/pRoloc/issues
Depends On Me	pRolocGUI
Imports Me
Suggests Me	MSnbase, pRolocdata, RforProteomics
Build Report

Package Archives

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

Source Package	pRoloc_1.18.0.tar.gz
Windows Binary	pRoloc_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	pRoloc_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pRoloc
Package Short Url	http://bioconductor.org/packages/pRoloc/
Package Downloads Report	Download Stats