HCATonsilData

DOI: 10.18129/B9.bioc.HCATonsilData  

Provide programmatic access to the tonsil cell atlas datasets

Bioconductor version: Release (3.18)

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] , Federico Marini [aut] , Alan O'Callaghan [aut], Helena L. Crowell [aut]

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

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	HCATonsilData
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SingleCellData, SpatialData
Version	1.0.0
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	ExperimentHub, SingleCellExperiment, SpatialExperiment, HDF5Array, SummarizedExperiment, S4Vectors, htmltools, rmarkdown, base64enc, utils
LinkingTo
Suggests	knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/massonix/HCATonsilData
BugReports	https://github.com/massonix/HCATonsilData/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HCATonsilData_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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