CSOA
This is the development version of CSOA; to use it, please install the devel version of Bioconductor.
Calculate per-cell gene signature scores using cell set overlaps
Bioconductor version: Development (3.22)
Cell Set Overlap Analysis (CSOA) is a tool for calculating per-cell gene signature scores in a 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.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica at foxmail.com>
citation("CSOA")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("CSOA")
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("CSOA")| Advanced CSOA | HTML | R Script |
| Getting started with CSOA | HTML | R Script |
| The CSOA algorithm | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | bayesbio, dplyr, ggeasy, ggforce, ggnewscale, ggplot2, ggraph, ggrepel, graphics, grDevices, kerntools, methods, qs, reshape2, Seurat, SeuratObject, SingleCellExperiment, SummarizedExperiment, sgof, spatstat.utils, stats, textshape, tidygraph, viridis, wesanderson |
| System Requirements | |
| URL | https://github.com/andrei-stoica26/CSOA |
| Bug Reports | https://github.com/andrei-stoica26/CSOA/issues |
See More
| Suggests | BiocStyle, knitr, patchwork, rmarkdown, scRNAseq, scuttle, stringr, 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 | CSOA_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | CSOA_0.99.2.tgz |
| macOS Binary (arm64) | CSOA_0.99.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CSOA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CSOA |
| Bioc Package Browser | https://code.bioconductor.org/browse/CSOA/ |
| Package Short Url | https://bioconductor.org/packages/CSOA/ |
| Package Downloads Report | Download Stats |