celldex
This is the development version of celldex; for the stable release version, see celldex.
Index of Reference Cell Type Datasets
Bioconductor version: Development (3.24)
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("celldex")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData |
| Version | 1.23.0 |
| 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 | augere.solo, ontoProc, scDiagnostics, scGraphVerse, 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_1.23.0.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 |