OSTA.data
This is thereleased version of OSTA.data; for the devel version, seeOSTA.data.
OSTA book data
Bioconductor version: Release (3.22)
'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("OSTA.data")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("OSTA.data")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport,DataRepresentation,ExperimentHubSoftware,GeneExpression,ImmunoOncology,Infrastructure,SingleCell,Software,Spatial,Transcriptomics |
| Version | 1.2.1 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 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 |
See More
| Suggests | BiocStyle,DropletUtils,knitr,VisiumIO,SpatialExperimentIO |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | ggspavis |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | OSTA.data_1.2.1.tar.gz |
| Windows Binary (x86_64) | OSTA.data_1.2.0.zip |
| macOS Binary (x86_64) | OSTA.data_1.2.1.tgz |
| macOS Binary (arm64) | OSTA.data_1.2.1.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/OSTA.data/ |
| Package Short Url | https://bioconductor.org/packages/OSTA.data/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.22 | Source Archive |