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Bioconductor - SpaceMarkers

SpaceMarkers

This is the released version of SpaceMarkers; for the devel version, see SpaceMarkers.

Spatial Interaction Markers

Bioconductor version: Release (3.21)

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] ORCID: 0000-0001-5144-6924 , Ludmila Danilova [ctb], Dmitrijs Lvovs [ctb] ORCID: 0009-0003-2152-6853

Maintainer: Atul Deshpande <adeshpande at jhu.edu>

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

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("SpaceMarkers")

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("SpaceMarkers")

Details biocViews GeneExpression, SingleCell, Software, Spatial, Transcriptomics Version 1.4.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License MIT + file LICENSE Depends R (>= 4.4.0) Imports matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix, qvalue, stats, utils, methods, ggplot2, reshape2 System Requirements URL https://github.com/DeshpandeLab/SpaceMarkers Bug Reports https://github.com/DeshpandeLab/SpaceMarkers/issues See More Suggests data.table, devtools, dplyr, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS Linking To Enhances BiocParallel 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.

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