plaid

This is the released version of plaid; for the devel version, see plaid.

All versions

3.24 (devel), 3.23 (release)

PLAID ultrafast gene set enrichment scoring

Bioconductor version: Release (3.23)

PLAID (Pathway Level Average Intensity Detection) is an ultra-fast method to compute single-sample enrichment scores for gene expression or proteomics data. For each sample, plaid computes the gene set score as the average intensity of the genes/proteins in the gene set. The output is a gene set score matrix suitable for further analyses.

Author: Ivo Kwee [aut] ORCID: 0000-0002-2751-4218 , Antonino Zito [cre] ORCID: 0000-0003-1931-984X

Maintainer: Antonino Zito <antonino.zito at bigomics.ch>

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

Ivo Kwee. plaid: PLAID ultrafast gene set enrichment scoring. doi:10.18129/B9.bioc.plaid, R package version 1.0.1, https://bioconductor.org/packages/plaid.

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")

BiocManager::install("plaid")

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("plaid")

Comparing PLAID with other methods	HTML	R Script
Getting Started with PLAID	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneSetEnrichment, Proteomics, Software
Version	1.0.1
In Bioconductor since	BioC 3.23 (R-4.6) (< 6 months)
License	GPL-3
Depends	R (>= 4.3.3)
Imports	Matrix, MatrixGenerics, matrixStats, methods, collapse, qlcMatrix, GSVA, fgsea, SummarizedExperiment, BiocSet, stats, utils
System Requirements
URL	https://github.com/bigomics/plaid https://bigomics.github.io/plaid/
Bug Reports	https://github.com/bigomics/plaid/issues

Suggests	BiocStyle, knitr, rmarkdown, sparseMatrixStats, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	plaid_1.0.1.tar.gz
Windows Binary (x86_64)	plaid_1.0.1.zip
macOS Binary (big-sur-x86_64)	plaid_1.0.1.tgz
macOS Binary (sonoma-arm64)	plaid_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/plaid
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/plaid
Package Short Url	https://bioconductor.org/packages/plaid/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive