SpaceMarkers
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 jhu.edu>
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 | ||
NEWS | Text | |
LICENSE | Text |
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 |
See More
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 | 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 |