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Spatial Interaction Markers

Bioconductor version: Release (3.19)

Spatial transcriptomic technologies have helped to resolve the connection between gene expression and the 2D orientation of tissues relative to each other. However, the limited single-cell resolution makes it difficult to highlight the most important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software, can help to find molecular interactions, by identifying genes associated with latent space interactions in spatial transcriptomics.

Author: Atul Deshpande [aut, cre] , Ludmila Danilova [ctb], Dimitrijs Lvovs [ctb]

Maintainer: Atul Deshpande <adeshpande at>

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


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if (!require("BiocManager", quietly = TRUE))


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Inferring Immune Interactions in Breast Cancer HTML R Script
Reference Manual PDF


biocViews GeneExpression, SingleCell, Software, Spatial, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4.0)
Imports matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, jsonlite, Matrix, qvalue, stats, utils, methods
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Suggests data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS
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Source Package SpaceMarkers_1.0.0.tar.gz
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macOS Binary (x86_64) SpaceMarkers_1.0.0.tgz
macOS Binary (arm64) SpaceMarkers_1.0.0.tgz
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