HDCytoData
This is the development version of HDCytoData; for the stable release version, see HDCytoData.
Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
Bioconductor version: Development (3.21)
Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state).
Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut]
Maintainer: Lukas M. Weber <lmweberedu at gmail.com>
citation("HDCytoData")):
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("HDCytoData")
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("HDCytoData")| 1. HDCytoData package | HTML | R Script |
| 2. Examples and use cases | HTML | R Script |
| 3. Contribution guidelines | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, FlowCytometryData, Homo_sapiens_Data, ImmunoOncologyData, SingleCellData |
| Version | 1.25.0 |
| License | MIT + file LICENSE |
| Depends | ExperimentHub, SummarizedExperiment, flowCore |
| Imports | utils, methods |
| System Requirements | |
| URL | https://github.com/lmweber/HDCytoData |
| Bug Reports | https://github.com/lmweber/HDCytoData/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust |
| Linking To | |
| Enhances | |
| Depends On Me | cytofWorkflow |
| Imports Me | |
| Suggests Me | CytoMDS, diffcyt, tidyFlowCore, tidytof |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HDCytoData_1.25.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/HDCytoData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HDCytoData |
| Package Short Url | https://bioconductor.org/packages/HDCytoData/ |
| Package Downloads Report | Download Stats |