plaid
This is the development version of plaid; to use it, please install the devel version of Bioconductor.
PLAID ultrafast gene set enrichment scoring
Bioconductor version: Development (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]
, Antonino Zito [cre]
Maintainer: Antonino Zito <antonino.zito at bigomics.ch>
citation("plaid")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Proteomics, Software |
| Version | 0.99.19 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.3.3) |
| Imports | Matrix, MatrixGenerics, matrixStats, methods, parallel, Rfast, 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | plaid_0.99.19.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/plaid |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/plaid |
| Bioc Package Browser | https://code.bioconductor.org/browse/plaid/ |
| Package Short Url | https://bioconductor.org/packages/plaid/ |
| Package Downloads Report | Download Stats |