DOI: 10.18129/B9.bioc.SPOTlight  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SPOTlight.

`SPOTlight`: Spatial Transcriptomics Deconvolution

Bioconductor version: 3.16

`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 "4.2") 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:



HTML R Script SPOTlight
PDF   Reference Manual
Text   NEWS


biocViews SingleCell, Software, Spatial, StatisticalMethod
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
License GPL-3
Depends R (>= 4.1)
Imports ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, stats
Suggests BiocStyle, colorBlindness, ExperimentHub, DelayedArray, ggcorrplot, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, Seurat, SeuratObject, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SPOTlight_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64) SPOTlight_1.2.0.tgz
macOS Binary (arm64) SPOTlight_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: