OSTA.data

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21

OSTA book data

Bioconductor version: Release (3.23)

'OSTA.data' is a companion package for the "Orchestrating Spatial Transcriptomics Analysis" (OSTA) with Bioconductor online book. Throughout OSTA, we rely on a set of publicly available datasets that cover different sequencing- and imaging-based platforms, such as Visium, Visium HD, Xenium (10x Genomics) and CosMx (NanoString). In addition, we rely on scRNA-seq (Chromium) data for tasks, e.g., spot deconvolution and label transfer (i.e., supervised clustering). These data been deposited in an Open Storage Framework (OSF) repository, and can be queried and downloaded using functions from the 'osfr' package. For convenience, we have implemented 'OSTA.data' to query and retrieve data from our OSF node, and cache retrieved Zip archives using 'BiocFileCache'.

Author: Yixing E. Dong [aut, cre] ORCID: 0009-0003-5115-5686 , Helena L. Crowell [aut] ORCID: 0000-0002-4801-1767 , Vince Carey [aut] ORCID: 0000-0003-4046-0063

Maintainer: Yixing E. Dong <estelladong729 at gmail.com>

Citation (from within R, enter citation("OSTA.data")):

Yixing E. Dong, Helena L. Crowell, Vince Carey. OSTA.data: OSTA book data. doi:10.18129/B9.bioc.OSTA.data, R package version 1.4.0, https://bioconductor.org/packages/OSTA.data.

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("OSTA.data")

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("OSTA.data")

OSTA.data	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, ExperimentHubSoftware, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.21 (R-4.5) (1.5 years)
License	Artistic-2.0
Depends	R (>= 4.5)
Imports	osfr, utils, BiocFileCache
System Requirements
URL	https://github.com/estellad/OSTA.data
Bug Reports	https://github.com/estellad/OSTA.data

Suggests	BiocStyle, DropletUtils, knitr, VisiumIO, SpatialExperimentIO
Linking To
Enhances
Depends On Me
Imports Me	OSTA
Suggests Me	Battlefield, ggspavis, SpatialFeatureExperiment
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	OSTA.data_1.4.0.tar.gz
Windows Binary (x86_64)	OSTA.data_1.4.0.zip
macOS Binary (big-sur-x86_64)	OSTA.data_1.4.0.tgz
macOS Binary (sonoma-arm64)	OSTA.data_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/OSTA.data
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OSTA.data
Package Short Url	https://bioconductor.org/packages/OSTA.data/
Package Downloads Report	Download Stats