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("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 | ||
| NEWS | Text |
Details
| biocViews | SingleCell, Software, Spatial, StatisticalMethod |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPOTlight_1.8.0.tar.gz |
| Windows Binary (x86_64) | 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 |