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`SPOTlight`: Spatial Transcriptomics Deconvolution

Bioconductor version: Release (3.19)

`SPOTlight`provides a method to deconvolute spatial transcriptomics spots using a seeded NMF approach along with visualization tools to assess the results. Spatially resolved gene expression profiles are key to understand tissue organization and function. However, novel spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots).

Author: Marc Elosua-Bayes [aut, cre], Helena L. Crowell [aut]

Maintainer: Marc Elosua-Bayes <elosua.marc at>

Citation (from within R, enter citation("SPOTlight")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

SPOTlight HTML R Script
Reference Manual PDF


biocViews SingleCell, Software, Spatial, StatisticalMethod
Version 1.8.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.1)
Imports ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, sparseMatrixStats, stats
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Suggests BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat
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Source Package SPOTlight_1.8.0.tar.gz
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macOS Binary (x86_64) SPOTlight_1.8.0.tgz
macOS Binary (arm64) SPOTlight_1.8.0.tgz
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