plaid
This is the released version of plaid; for the devel version, see plaid.
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]
, Antonino Zito [cre]
Maintainer: Antonino Zito <antonino.zito at bigomics.ch>
citation("plaid")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Proteomics, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | plaid_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | plaid_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | plaid_1.0.0.tgz |
| 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 |