celldex
This is the development version of celldex; for the stable release version, see celldex.
Index of Reference Cell Type Datasets
Bioconductor version: Development (3.21)
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("celldex")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData |
| Version | 1.15.0 |
| 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.workflows, SingleRBook |
| Imports Me | singleCellTK |
| Suggests Me | ontoProc, scDiagnostics, SingleR, sketchR, tidySingleCellExperiment |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | celldex_1.15.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |