To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("pRoloc")
In most cases, you don't need to download the package archive at all.
pRoloc
A unifying bioinformatics framework for spatial proteomics
Bioconductor version: 3.0
This package implements pattern recognition techniques on quantitiative mass spectrometry data to 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>
Citation (from within R,
enter citation("pRoloc")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("pRoloc")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pRoloc")
| R Script | A state-of-the-art machine learning pipeline for the analysis of spatial proteomics data | |
| R Script | Machine learning techniques available in pRoloc | |
| R Script | pRoloc -- A unifying bioinformatics framework for organelle proteomics | |
| R Script | pRoloc tutorial | |
| Reference Manual | ||
| Text | README | |
| Text | NEWS | |
| Video | pRoloc, pRolocdata and pRolocGUI |
Details
| biocViews | Classification, Clustering, MassSpectrometry, Proteomics, QualityControl, Software |
| Version | 1.6.2 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | GPL-2 |
| Depends | R (>= 2.15), MSnbase(>= 1.13.3), MLInterfaces(>= 1.37.1), methods, Rcpp (>= 0.10.3), BiocParallel |
| Imports | mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, BiocGenerics, stats, RColorBrewer, scales, MASS, knitr, mvtnorm |
| LinkingTo | Rcpp, RcppArmadillo |
| Suggests | testthat, pRolocdata, roxygen2, synapter, xtable |
| SystemRequirements | |
| Enhances | |
| URL | |
| 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.
| Package Source | pRoloc_1.6.2.tar.gz |
| Windows Binary | pRoloc_1.6.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | pRoloc_1.6.2.tgz |
| Mac OS X 10.9 (Mavericks) | pRoloc_1.6.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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