CSOA
Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps
Bioconductor version: 3.24 · Package version: 1.3.3
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Cell Set Overlap Analysis (CSOA) is a tool for calculating per-cell gene signature scores in an scRNA-seq dataset. CSOA constructs a set for each gene in the signature, consisting of the cells that highly express the gene. Next, all overlaps of pairs of cell sets are computed, ranked, filtered and scored. The CSOA per-cell score is calculated by summing up all products of the overlap scores and the min-max-normalized expression of the two involved genes. CSOA can run on a Seurat object, a SingleCellExperiment object, a matrix and a dgCMatrix.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CSOA")Details
| Maintainer | Andrei-Florian Stoica <andreistoica@foxmail.com> |
| Author | Andrei-Florian Stoica [aut, cre] (ORCID: <https://orcid.org/0000-0002-5253-0826>) |
| License | MIT + file LICENSE |
| URL | https://github.com/andrei-stoica26/CSOA |
| Bug Reports | https://github.com/andrei-stoica26/CSOA/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/CSOA/ |
Citation
From within R, enter citation("CSOA"):
Andrei-Florian Stoica. CSOA: Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps. doi:10.18129/B9.bioc.CSOA, R package version 1.3.3, https://bioconductor.org/packages/CSOA.
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 | CSOA_1.3.3.tar.gz |
| Windows binary (x86_64) | CSOA_1.3.3.zip |
| macOS binary (arm64) | CSOA_1.3.3.tgz |
| macOS binary (x86_64) | CSOA_1.3.3.tgz |
Dependencies
Imports: dplyr, ggplot2, henna, kerntools, methods, paletteer, qs2, reshape2, rlang, Seurat, SeuratObject, SummarizedExperiment, spatstat.utils, stats, textshape
Suggests: BiocStyle, knitr, patchwork, rmarkdown, scRNAseq, scuttle, stringr, testthat (>= 3.0.0)
Reverse dependencies
Imports Me (1): GSABenchmark