Cepo

DOI: 10.18129/B9.bioc.Cepo  

Cepo for the identification of differentially stable genes

Bioconductor version: Release (3.16)

Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.

Author: Hani Jieun Kim [aut, cre] , Kevin Wang [aut]

Maintainer: Hani Jieun Kim <hani.kim127 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Cepo")

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("Cepo")

 

HTML	R Script	Cepo method for differential stability analysis of scRNA-seq data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	MIT + file LICENSE
Depends	GSEABase, R (>= 4.1)
Imports	DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap, patchwork
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	scClassify
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Cepo_1.4.0.tar.gz
Windows Binary	Cepo_1.4.0.zip
macOS Binary (x86_64)	Cepo_1.4.0.tgz
macOS Binary (arm64)	Cepo_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Cepo
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Cepo
Bioc Package Browser	https://code.bioconductor.org/browse/Cepo/
Package Short Url	https://bioconductor.org/packages/Cepo/
Package Downloads Report	Download Stats