HCATonsilData
This is the development version of HCATonsilData; for the stable release version, see HCATonsilData.
Provide programmatic access to the tonsil cell atlas datasets
Bioconductor version: Development (3.21)
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:
Maintainer: Ramon Massoni-Badosa <ramonmassoni at gmail.com>
citation("HCATonsilData")):
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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SingleCellData, SpatialData |
| Version | 1.3.0 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HCATonsilData_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |