celldex

Index of Reference Cell Type Datasets


Bioconductor version: Release (3.19)

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 D√ľndar [aut]

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

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

Installation

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


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

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

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData
Version 1.14.0
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/
See More
Suggests testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate, BiocManager, ensembldb
Linking To
Enhances
Depends On Me OSCA.basic, OSCA.workflows, SingleRBook
Imports Me singleCellTK
Suggests Me ontoProc, SingleR, sketchR, tidySingleCellExperiment, tidySpatialExperiment
Links To Me
Build Report Build Report

Package Archives

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

Source Package celldex_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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