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 (3.20)
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("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 | ||
NEWS | Text | |
pRoloc, pRolocdata and pRolocGUI | Video |
Details
biocViews | Classification, Clustering, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software |
Version | 1.45.1 |
In Bioconductor since | BioC 2.12 (R-3.0) (11.5 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 |
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_1.45.1.tar.gz |
Windows Binary | pRoloc_1.45.1.zip (64-bit only) |
macOS Binary (x86_64) | pRoloc_1.45.1.tgz |
macOS Binary (arm64) | pRoloc_1.45.1.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 |