celaref
This is the development version of celaref; for the stable release version, see celaref.
Single-cell RNAseq cell cluster labelling by reference
Bioconductor version: Development (3.24)
After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).
Author: Sarah Williams [aut, cre]
Maintainer: Sarah Williams <sarah.williams1 at monash.edu>
citation("celaref")):
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("celaref")
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("celaref")| Manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | SingleCell, Software |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), SummarizedExperiment |
| Imports | MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray |
| System Requirements | |
| URL |
See More
| Suggests | limma, parallel, knitr, rmarkdown, ExperimentHub, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | celaref_1.31.0.tar.gz |
| Windows Binary (x86_64) | celaref_1.31.0.zip |
| macOS Binary (big-sur-x86_64) | celaref_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | celaref_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/celaref |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/celaref |
| Bioc Package Browser | https://code.bioconductor.org/browse/celaref/ |
| Package Short Url | https://bioconductor.org/packages/celaref/ |
| Package Downloads Report | Download Stats |