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SPOTlight

`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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SPOTlight")

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

Documentation

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

browseVignettes("SPOTlight")
SPOTlight HTML R Script
Reference Manual PDF
NEWS Text

Details

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
System Requirements
URL https://github.com/MarcElosua/SPOTlight
Bug Reports https://github.com/MarcElosua/SPOTlight/issues
See More
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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Package Archives

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

Source Package SPOTlight_1.8.0.tar.gz
Windows Binary SPOTlight_1.8.0.zip (64-bit only)
macOS Binary (x86_64) SPOTlight_1.8.0.tgz
macOS Binary (arm64) SPOTlight_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SPOTlight
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SPOTlight
Bioc Package Browser https://code.bioconductor.org/browse/SPOTlight/
Package Short Url https://bioconductor.org/packages/SPOTlight/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive