getRDS: Download a processed sample from our S3 bucket

In edward130603/BayesSpace: Clustering and Resolution Enhancement of Spatial Transcriptomes

Download a processed sample from our S3 bucket

Description

Datasets are cached locally using BiocFileCache. The first time using this function, you may need to consent to creating a BiocFileCache directory if one does not already exist.

Usage

getRDS(dataset, sample, cache = TRUE)

Arguments

dataset	Dataset identifier
sample	Sample identifier
cache	If true, cache the dataset locally with BiocFileCache. Otherwise, download directly from our S3 bucket. Caching saves time on subsequent loads, but consumes disk space.

Details

The following datasets are available via getRDS.

Dataset	Sample(s)
2018_thrane_melanoma	ST_mel1_rep2
2020_maynard_prefrontal-cortex	151507, 151508, 151509, 151510, 151669, 151670, 151671, 151672, 151673, 151674, 151675, 151676
2020_ji_squamous-cell-carcinoma	P4_rep1
2020_10X-IDC	IDC1
2020_10X-demo_ovarian-cancer	whole_transcriptome

Value

sce A SingleCellExperiment with positional information in colData and PCs based on the top 2000 HVGs

Examples

sce <- getRDS("2018_thrane_melanoma", "ST_mel1_rep2", cache = FALSE)

edward130603/BayesSpace documentation built on May 11, 2023, 6:13 a.m.