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Cepo

This is the development version of Cepo; for the stable release version, see Cepo.

Cepo for the identification of differentially stable genes

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("Cepo")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Classification, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version 1.7.0
In Bioconductor since BioC 3.14 (R-4.1) (2 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
Linking To
Suggests knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap, patchwork
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Depends On Me
Imports Me scClassify
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Package Archives

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

Source Package Cepo_1.7.0.tar.gz
Windows Binary Cepo_1.7.0.zip (64-bit only)
macOS Binary (x86_64) Cepo_1.7.0.tgz
macOS Binary (arm64)
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