Bioconductor – Cepo (development version)

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 (3.17)

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")

 

HTML

R Script

Cepo method for differential stability analysis of scRNA-seq data
PDF   Reference Manual

Details

biocViews Classification, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version 1.5.0
In Bioconductor since BioC 3.14 (R-4.1) (1 year)
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  

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instructions to use this
package in your R session.


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