celaref

DOI: 10.18129/B9.bioc.celaref    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see celaref.

Single-cell RNAseq cell cluster labelling by reference

Bioconductor version: 3.9

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 "3.6") 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 SingleCell, Software
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (1 year)
License GPL-3
Depends R (>= 3.5.0), SummarizedExperiment
Imports MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray
LinkingTo
Suggests limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
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_1.2.0.tar.gz
Windows Binary celaref_1.2.0.zip
Mac OS X 10.11 (El Capitan) celaref_1.2.0.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 https://bioconductor.org/packages/celaref/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: