Cepo

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see Cepo.

Cepo for the identification of differentially stable genes

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software

Version 1.8.0

In Bioconductor since BioC 3.14 (R-4.1) (2.5 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

System Requirements

URL

Suggests knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap, patchwork

Linking To

Enhances

Depends On Me

Imports Me scClassify

Suggests Me

Links To Me

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Package Archives

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

Source Package Cepo_1.8.0.tar.gz

Windows Binary Cepo_1.8.0.zip

macOS Binary (x86_64) Cepo_1.8.0.tgz

macOS Binary (arm64) Cepo_1.8.0.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/

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