bc: Human Breast Cancer (BC) Dataset

In estfernan/boost: Bayesian Modeling of Spatial Transcriptomics Data

Human Breast Cancer (BC) Dataset

Description

The human breast cancer (BC) study is a publicly available ST dataset accessible on the Spatial Research Lab http://www.spatialresearch.org. There are four layers in the BC study. Following the previous studies (Li et al., 2020; Sun et al., 2020; Svensson et al., 2018), the BC layer 2, which contains 14,789 genes measured on 250 spots, was saved.

Format

bc is a matrix with 250 spots and 14,789 genes that denotes the expression count table. bc.spots is a matrix of the geospatial profile.

Source

Publicly available at http://www.spatialresearch.org.

References

Li, Q., M. Zhang, Y. Xie, and G. Xiao (2020). Bayesian modeling of spatial molecular profiling data via Gaussian process. arXiv preprint arXiv:2012.03326.

Sun, S., J. Zhu, and X. Zhou (2020). Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies. Nature Methods 17 (2), 193–200.

Svensson, V., S. A. Teichmann, and O. Stegle (2018). SpatialDE: Identification of spatially variable genes. Nature Methods 15 (5), 343–346.

Examples

## human breast cancer (BC) dataset
data(bc)

estfernan/boost documentation built on June 24, 2022, 12:20 a.m.