AUCell
This is the development version of AUCell; for the stable release version, see AUCell.
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
Bioconductor version: Development (3.24)
AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.
Author: Sara Aibar, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium.
Maintainer: Gert Hulselmans <Gert.Hulselmans at kuleuven.be>
citation("AUCell")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("AUCell")
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("AUCell")| AUCell: Identifying cells with active gene sets | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Normalization, SingleCell, Software, Transcription, Transcriptomics, WorkflowStep |
| Version | 1.35.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | GPL-3 |
| Depends | |
| Imports | DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils |
| System Requirements | |
| URL | http://scenic.aertslab.org |
See More
| Suggests | Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo |
| Linking To | |
| Enhances | doMC, doRNG, doParallel, foreach |
| Depends On Me | OSCA.basic |
| Imports Me | scFeatures, OSTA |
| Suggests Me | decoupleR, escape, GSABenchmark, pathMED, scDiagnostics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AUCell_1.35.0.tar.gz |
| Windows Binary (x86_64) | AUCell_1.35.0.zip |
| macOS Binary (big-sur-x86_64) | AUCell_1.35.0.tgz |
| macOS Binary (sonoma-arm64) | AUCell_1.35.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AUCell |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AUCell |
| Bioc Package Browser | https://code.bioconductor.org/browse/AUCell/ |
| Package Short Url | https://bioconductor.org/packages/AUCell/ |
| Package Downloads Report | Download Stats |