pRoloc
This is the released version of pRoloc; for the devel version, see pRoloc.
A unifying bioinformatics framework for spatial proteomics
Bioconductor version: Release (3.23)
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("pRoloc")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 |
| 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 | 1.52.0 |
| 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 |
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, 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pRoloc_1.52.0.tar.gz |
| Windows Binary (x86_64) | pRoloc_1.52.0.zip |
| macOS Binary (big-sur-x86_64) | pRoloc_1.52.0.tgz |
| macOS Binary (sonoma-arm64) | pRoloc_1.52.0.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 |