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 (3.24)
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("Cepo")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.19.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (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, 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_1.19.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | Cepo_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | Cepo_1.19.0.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/ |
| Package Downloads Report | Download Stats |