SpaceMarkers
This is the development version of SpaceMarkers; for the stable release version, see SpaceMarkers.
Spatial Interaction Markers
Bioconductor version: Development (3.24)
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] 
, Orian Stapleton [aut], Ludmila Danilova [ctb], Dmitrijs Lvovs [ctb]
Maintainer: Atul Deshpande <adeshpande at jhu.edu>
citation("SpaceMarkers")):Atul Deshpande, Orian Stapleton. SpaceMarkers: Spatial Interaction Markers. doi:10.18129/B9.bioc.SpaceMarkers, R package version 2.3.1, https://bioconductor.org/packages/SpaceMarkers.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 |
| SpaceMarkers with SpatialExperiment Objects | HTML | R Script |
| SpaceMarkers Functions Step-by-Step | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 2.3.1 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix, qvalue, stats, utils, methods, ggplot2, reshape2, RColorBrewer, circlize, mixtools, dplyr, readbitmap, rlang, effsize, viridis |
| System Requirements | |
| URL | https://github.com/DeshpandeLab/SpaceMarkers |
| Bug Reports | https://github.com/DeshpandeLab/SpaceMarkers/issues |
See More
| Suggests | data.table, devtools, knitr, cowplot, rjson, rmarkdown, BiocStyle, BiocFileCache, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap, zellkonverter, anndataR |
| Linking To | |
| Enhances | BiocParallel |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpaceMarkers_2.3.1.tar.gz |
| Windows Binary (x86_64) | SpaceMarkers_2.3.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SpaceMarkers_2.3.1.tgz |
| macOS Binary (sonoma-arm64) | SpaceMarkers_2.3.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpaceMarkers |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpaceMarkers |
| Package Short Url | https://bioconductor.org/packages/SpaceMarkers/ |
| Package Downloads Report | Download Stats |