plaid
PLAID ultrafast gene set enrichment scoring
Bioconductor version: 3.23 · Package version: 1.0.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("plaid")Details
| Maintainer | Antonino Zito <antonino.zito@bigomics.ch> |
| Author | Ivo Kwee [aut] (ORCID: <https://orcid.org/0000-0002-2751-4218>), Antonino Zito [cre] (ORCID: <https://orcid.org/0000-0003-1931-984X>) |
| License | GPL-3 |
| URL | https://github.com/bigomics/plaid, https://bigomics.github.io/plaid/ |
| Bug Reports | https://github.com/bigomics/plaid/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GeneSetEnrichment, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/plaid/ |
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.
Documentation
Download
Follow the 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 (arm64) | plaid_1.0.1.tgz |
| macOS binary (x86_64) | plaid_1.0.1.tgz |
Dependencies
Depends: R (>= 4.3.3)
Imports: Matrix, MatrixGenerics, matrixStats, methods, collapse, qlcMatrix, GSVA, fgsea, SummarizedExperiment, BiocSet, stats, utils
Suggests: BiocStyle, knitr, rmarkdown, sparseMatrixStats, testthat (>= 3.0.0)