HCATonsilData

This is the released version of HCATonsilData; for the devel version, see HCATonsilData.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18

Provide programmatic access to the tonsil cell atlas datasets

Bioconductor version: Release (3.23)

This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.

Author: Ramon Massoni-Badosa [aut, cre] ORCID: 0000-0001-7115-8145 , Federico Marini [aut] ORCID: 0000-0003-3252-7758 , Alan O'Callaghan [aut], Helena L. Crowell [aut] ORCID: 0000-0002-4801-1767

Maintainer: Ramon Massoni-Badosa <ramonmassoni at gmail.com>

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

Ramon Massoni-Badosa, Federico Marini, Alan O'Callaghan, Helena L. Crowell. HCATonsilData: Provide programmatic access to the tonsil cell atlas datasets. doi:10.18129/B9.bioc.HCATonsilData, R package version 1.10.0, https://bioconductor.org/packages/HCATonsilData.

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")

BiocManager::install("HCATonsilData")

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("HCATonsilData")

HCATonsilData	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SingleCellData, SpatialData
Version	1.10.0
In Bioconductor since	BioC 3.18 (R-4.3) (3 years)
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	ExperimentHub, SingleCellExperiment, SpatialExperiment, HDF5Array, SummarizedExperiment, S4Vectors, htmltools, rmarkdown, base64enc, utils
System Requirements
URL	https://github.com/massonix/HCATonsilData
Bug Reports	https://github.com/massonix/HCATonsilData/issues

Suggests	knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	HCATonsilData_1.10.0.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/HCATonsilData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HCATonsilData
Package Short Url	https://bioconductor.org/packages/HCATonsilData/
Package Downloads Report	Download Stats