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 (3.21)
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] (ORCID:
Maintainer: Hani Jieun Kim <hani.kim127 at gmail.com>
citation("Cepo")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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, purrr |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | scClassify |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Cepo_1.13.0.tar.gz |
| Windows Binary (x86_64) | Cepo_1.13.0.zip |
| macOS Binary (x86_64) | Cepo_1.13.0.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 |