Package: SPOTlight 1.11.0
Marc Elosua-Bayes
SPOTlight: `SPOTlight`: Spatial Transcriptomics Deconvolution
`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).
Authors:
SPOTlight_1.11.0.tar.gz
SPOTlight_1.11.0.zip(r-4.5)SPOTlight_1.11.0.zip(r-4.4)SPOTlight_1.11.0.zip(r-4.3)
SPOTlight_1.11.0.tgz(r-4.5-any)SPOTlight_1.11.0.tgz(r-4.4-any)SPOTlight_1.11.0.tgz(r-4.3-any)
SPOTlight_1.11.0.tar.gz(r-4.5-noble)SPOTlight_1.11.0.tar.gz(r-4.4-noble)
SPOTlight_1.11.0.tgz(r-4.4-emscripten)SPOTlight_1.11.0.tgz(r-4.3-emscripten)
SPOTlight.pdf |SPOTlight.html✨
SPOTlight/json (API)
NEWS
| # Install 'SPOTlight' in R: |
| install.packages('SPOTlight', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/marcelosua/spotlight/issues
On BioConductor:SPOTlight-1.11.0(bioc 3.21)SPOTlight-1.10.0(bioc 3.20)
singlecellspatialstatisticalmethod
Last updated 5 months agofrom:eae1ff58e0. Checks:4 OK, 3 NOTE, 1 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 28 2025 |
| R-4.5-win | NOTE | Feb 28 2025 |
| R-4.5-mac | NOTE | Feb 28 2025 |
| R-4.5-linux | NOTE | Feb 28 2025 |
| R-4.4-win | OK | Feb 28 2025 |
| R-4.4-mac | OK | Feb 28 2025 |
| R-4.3-win | OK | Feb 28 2025 |
| R-4.3-mac | ERROR | Feb 28 2025 |
Exports:getMGSmockSCmockSPplotCorrelationMatrixplotImageplotInteractionsplotSpatialScatterpieplotTopicProfilesrunDeconvolutionSPOTlighttrainNMF
Dependencies:abindaskpassBiobaseBiocGenericsBiocManagercliclustercodetoolscolorspacecrayoncurlDelayedArraydigestdoParallelfansifarverforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridBasegtablehttrIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeNMFnnlsopensslpillarpkgconfigplyrR6RColorBrewerRcppregistryreshape2rlangrngtoolsS4ArraysS4VectorsscalesSingleCellExperimentSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Synthetic single-cell, mixture and marker data | data getMGS mockSC mockSP |
| Plot Correlation Matrix | plotCorrelationMatrix |
| Plot JP(E)G/PNG/Raster/RGB images | plotImage |
| Plot group interactions | plotHeatmap plotInteractions plotNetwork |
| Spatial scatterpie | plotSpatialScatterpie |
| Plot NMF topic profiles | plotTopicProfiles |
| Run Deconvolution using NNLS model | runDeconvolution |
| Deconvolution of mixture using single-cell data | SPOTlight |
| train NMF model | trainNMF |
