SPOTlight

DOI: 10.18129/B9.bioc.SPOTlight    

`SPOTlight`: Spatial Transcriptomics Deconvolution

Bioconductor version: Release (3.15)

`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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	SPOTlight
PDF		Reference Manual
Text		NEWS

Details

biocViews	SingleCell, Software, Spatial, StatisticalMethod
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, stats
LinkingTo
Suggests	BiocStyle, colorBlindness, ExperimentHub, DelayedArray, ggcorrplot, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, Seurat, SeuratObject, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat
SystemRequirements
Enhances
URL	https://github.com/MarcElosua/SPOTlight
BugReports	https://github.com/MarcElosua/SPOTlight/issues
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_1.0.0.tar.gz
Windows Binary	SPOTlight_1.0.0.zip
macOS Binary (x86_64)	SPOTlight_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SPOTlight
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SPOTlight
Package Short Url	https://bioconductor.org/packages/SPOTlight/
Package Downloads Report	Download Stats