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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>

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

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")
HCATonsilData HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

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
System Requirements
URL https://github.com/massonix/HCATonsilData
Bug Reports https://github.com/massonix/HCATonsilData/issues
See More
Suggests knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle
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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/
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