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>
citation("celaref")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("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")| Manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, SingleCell, Software |
| Version | 1.0.1 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | limma, parallel, knitr, rmarkdown, ExperimentHub |
| 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_1.0.1.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/celaref/ |
| Package Short Url | https://bioconductor.org/packages/celaref/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |