Cepo

DOI: 10.18129/B9.bioc.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 (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews Classification, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License MIT + file LICENSE
Depends GSEABase, R (>= 4.1)
Imports DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/Cepo
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Cepo
Package Short Url https://bioconductor.org/packages/Cepo/
Package Downloads Report Download Stats

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