SpaceMarkers

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see SpaceMarkers.

Spatial Interaction Markers

Bioconductor version: 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 jhu.edu>

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

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

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
System Requirements
URL	https://github.com/atuldeshpande/SpaceMarkers
Bug Reports	https://github.com/atuldeshpande/SpaceMarkers/issues

Suggests	data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS
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	SpaceMarkers_1.0.0.tar.gz
Windows Binary (x86_64)	SpaceMarkers_1.0.0.zip
macOS Binary (x86_64)	SpaceMarkers_1.0.0.tgz
macOS Binary (arm64)	SpaceMarkers_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpaceMarkers
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpaceMarkers
Bioc Package Browser	https://code.bioconductor.org/browse/SpaceMarkers/
Package Short Url	https://bioconductor.org/packages/SpaceMarkers/
Package Downloads Report	Download Stats