# Introduction
<img src="inst/extdata/OSTA.data.png" width="200" align="right"/>
`OSTA.data` is a data retrieval package for all data used in the OSTA book. It conveniently loads raw data from Open Science Framework (OSF) to cache or local download.
# Installation
```r
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("estellad/OSTA.data")
```
# Usage
The following data are available to download in `library(OSTA.data)`
```r
OSTA.data_list()
# [1] "Chromium_HumanBreast_Janesick"
# [2] "Chromium_HumanColon_Oliveira"
# [3] "CosMx1k_MouseBrain1"
# [4] "CosMx1k_MouseBrain2"
# [5] "CosMx6k_HumanBrain"
# [6] "Visium_HumanBreast_Janesick"
# [7] "Visium_HumanColon_Oliveira"
# [8] "VisiumHD_HumanColon_Oliveira"
# [9] "Xenium_HumanBreast1_Janesick"
# [10] "Xenium_HumanColon_Oliveira"
```
Each data set can be retrieved and unzipped. List necessary raw data files available with `list.files(td)`.
```r
pa <- OSTA.data_load("Xenium_HumanColon_Oliveira")
# unpacking
dir.create(td <- tempfile())
unzip(pa, exdir=td)
```
After download, import data as a `SpatialExperiment` object with [`library(SpatialExperimentIO)`](https://github.com/estellad/SpatialExperimentIO).
```r
library(SpatialExperimentIO)
(spe <- readXeniumSXE(td))
# class: SpatialExperiment
# dim: 541 340837
# metadata(3): transcripts cell_boundaries nucleus_boundaries
# assays(1): counts
# rownames(541): ABCC8 ACP5 ... UnassignedCodeword_0330 UnassignedCodeword_0338
# rowData names(3): ID Symbol Type
# colnames(340837): aaaadaba-1 aaaadgga-1 ... oikdmkkf-1 oikeebja-1
# colData names(10): cell_id transcript_counts ... nucleus_area sample_id
# reducedDimNames(0):
# mainExpName: NULL
# altExpNames(0):
# spatialCoords names(2) : x_centroid y_centroid
# imgData names(0):
```
