celldex

This is the development version of celldex; for the stable release version, see celldex.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

Index of Reference Cell Type Datasets

Bioconductor version: Development (3.24)

Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.

Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut], Jared Andrews [aut], Friederike Dündar [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("celldex")):

Dvir Aran, Aaron Lun, Daniel Bunis, Jared Andrews, Friederike Dündar. celldex: Index of Reference Cell Type Datasets. doi:10.18129/B9.bioc.celldex, R package version 1.23.0, https://bioconductor.org/packages/celldex.

Generated from the package metadata; it may differ from the package's own citation.

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("celldex")

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("celldex")

Cell type references	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData
Version	1.23.0
In Bioconductor since	BioC 3.12 (R-4.0) (6 years)
License	GPL-3
Depends	SummarizedExperiment
Imports	utils, methods, Matrix, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats, gypsum, alabaster.base, alabaster.matrix, alabaster.se, DBI, RSQLite, jsonlite
System Requirements
URL	https://github.com/LTLA/celldex
Bug Reports	https://support.bioconductor.org/

Suggests	testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate, BiocManager, ensembldb
Linking To
Enhances
Depends On Me	OSCA.workflows, SingleRBook
Imports Me	singleCellTK
Suggests Me	augere.solo, ontoProc, scCertify, scDiagnostics, scGraphVerse, SingleR, sketchR, tidySingleCellExperiment
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	celldex_1.23.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/celldex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/celldex
Package Short Url	https://bioconductor.org/packages/celldex/
Package Downloads Report	Download Stats