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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 (3.19)

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 (from within R, enter citation("celaref")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF
NEWS Text

Details

biocViews SingleCell, Software
Version 1.21.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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
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Suggests limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
Linking To
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Build Report Build Report

Package Archives

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

Source Package celaref_1.21.0.tar.gz
Windows Binary celaref_1.21.0.zip
macOS Binary (x86_64) celaref_1.21.0.tgz
macOS Binary (arm64) celaref_1.21.0.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