pRoloc
A unifying bioinformatics framework for spatial proteomics
Bioconductor version: Release (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")
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 | 1.46.0 |
| 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(>= 1.43.2), roxygen2, xtable, rgl, BiocStyle(>= 2.5.19), hpar(>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick |
| 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_1.46.0.tar.gz |
| Windows Binary (x86_64) | pRoloc_1.46.0.zip |
| macOS Binary (x86_64) | pRoloc_1.46.0.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 |