SPOTlight

Spatial Transcriptomics Capture Location Deconvolution

MarcElosua
164
25
R

Welcome to SPOTlight

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Current build status

  • release Bioconductor Availability
    Bioconductor Dependencies
    Bioconductor Commits
    Bioconductor Release Build
  • development Bioconductor Availability
    Bioconductor Dependencies
    Bioconductor Commits
    Bioconductor Devel Build

We are currently on the process of submitting SPOTlight to bioconductor and there have been some styling changes on this branch compared to previous releases. If you want to use the version we are currently submitting feel free to look at the updated vignette here. If you want to keep using the previous versions, you can still find it in the spotlight-0.1.7 branch and follow the previous vignette.

SPOTlight provides a tool that enables the deconvolution of mixtures of cells from a single-cell reference. Originally developed for 10X’s Visium - spatial transcriptomics- technology, it can be used for all technologies that output mixtures of cells. It is compatible with Bioconductor’s SingleCellExperiment and SpatialExperiment classes as well as dense and sparse matrices. Furthermore, the package also provides visualization tools to assess the results of the deconvolution. Briefly, SPOTlight is based on finding topic profile signatures, by means of an NMFreg model, for each cell type and then optimizing the cell types proportions to fit the mixture we want to deconvolute.

Installation

install.packages("BiocManager")
BiocManager::install("SPOTlight")
# Or the devel version
BiocManager::install("SPOTlight", version = "devel")

Alternatively, you can install it from GitHub using the devtools package.

install.packages("devtools")
library(devtools)
install_github("https://github.com/MarcElosua/SPOTlight")

References

  • Elosua-Bayes M, Nieto P, Mereu E, Gut I, Heyn H (2021): SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes. Nucleic Acids Res 49(9):e50. doi:10.1093/nar/gkab043.

Contributors

SPOTlight was originally developed by Marc Elosua Bayes and has received substantial additional contributions from Helena L. Crowell.

Issues - Ideas?

SPOTlight is still under active development. We greatly welcome (and highly encourage!) all feedback, bug reports and suggestions for improvement here. Please make sure to raise issues with a reproducible example and the output of your sessionInfo().