Introduction

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

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)

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).

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).

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):