PrInCE

This is the development version of PrInCE; for the stable release version, see PrInCE.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

Predicting Interactomes from Co-Elution

Bioconductor version: Development (3.24)

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>

Citation (from within R, enter citation("PrInCE")):

Michael Skinnider, Leonard Foster. PrInCE: Predicting Interactomes from Co-Elution. doi:10.18129/B9.bioc.PrInCE, R package version 1.29.0, https://bioconductor.org/packages/PrInCE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	NetworkInference, Proteomics, Software, SystemsBiology
Version	1.29.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
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)
System Requirements
URL
Bug Reports	https://github.com/fosterlab/PrInCE/issues

Suggests	BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	PrInCE_1.29.0.tar.gz
Windows Binary (x86_64)	PrInCE_1.29.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	PrInCE_1.29.0.tgz
macOS Binary (sonoma-arm64)	PrInCE_1.29.0.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