celaref

DOI: 10.18129/B9.bioc.celaref    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see celaref.

Single-cell RNAseq cell cluster labelling by reference

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

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

 

HTML	R Script	Manual
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, SingleCell, Software
Version	1.0.1
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 years)
License	GPL-3
Depends	R (>= 3.5.0), SummarizedExperiment
Imports	MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble
LinkingTo
Suggests	limma, parallel, knitr, rmarkdown, ExperimentHub
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	celaref_1.0.1.tar.gz
Windows Binary	celaref_1.0.1.zip
Mac OS X 10.11 (El Capitan)	celaref_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/celaref
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/celaref
Package Short Url	http://bioconductor.org/packages/celaref/
Package Downloads Report	Download Stats