PrInCE

DOI: 10.18129/B9.bioc.PrInCE    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PrInCE.

Predicting Interactomes from Co-Elution

Bioconductor version: 3.9

PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.

Author: Michael Skinnider [aut, trl, cre], R. Greg Stacey [ctb], Nichollas Scott [ctb], Anders Kristensen [ctb], Leonard Foster [aut, led]

Maintainer: Michael Skinnider <michael.skinnider at msl.ubc.ca>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PrInCE")

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("PrInCE")

 

HTML	R Script	Interactome reconstruction from co-elution data with PrInCE
PDF		Reference Manual
Text		LICENSE

Details

biocViews	NetworkInference, Proteomics, Software, SystemsBiology
Version	1.0.1
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-3 + file LICENSE
Depends	R (>= 3.6.0)
Imports	purrr (>= 0.2.4), dplyr (>= 0.7.4), tidyr (>= 0.8.99), forecast (>= 8.2), progress (>= 1.1.2), Hmisc (>= 4.0), naivebayes (>= 0.9.1), robustbase (>= 0.92-7), ranger (>= 0.8.0), LiblineaR (>= 2.10-8), speedglm (>= 0.3-2), tester (>= 0.1.7), magrittr (>= 1.5), Biobase(>= 2.40.0), MSnbase(>= 2.8.3), stats, utils, methods, Rdpack (>= 0.7)
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/fosterlab/PrInCE/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	PrInCE_1.0.1.tar.gz
Windows Binary	PrInCE_1.0.1.zip
Mac OS X 10.11 (El Capitan)	PrInCE_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PrInCE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PrInCE
Package Short Url	https://bioconductor.org/packages/PrInCE/
Package Downloads Report	Download Stats