SpaceMarkers
This is the released version of SpaceMarkers; for the devel version, see SpaceMarkers.
Spatial Interaction Markers
Bioconductor version: Release (3.20)
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], Dmitrijs Lvovs [ctb]
Maintainer: Atul Deshpande <adeshpande at jhu.edu>
citation("SpaceMarkers")):
Deshpande, Atul, Loth, Melanie, Sidiropoulos, N. D, Zhang, Shuming, Yuan, Long, Bell, F. AT, Zhu, Qingfeng, Ho, Jin W, Santa-Maria, Cesar, Gilkes, M. D, Williams, R. S, Uytingco, R. C, Chew, Jennifer, Hartnett, Andrej, Bent, W. Z, Favorov, V. A, Popel, S. A, Yarchoan, Mark, Kiemen, Ashley, Wu, Pei-Hsun, Fujikura, Kohei, Wirtz, Denis, Wood, D. L, Zheng, Lei, Jaffee, M. E, Anders, A. R, Danilova, Ludmila, Stein-O’Brien, Genevieve, Kagohara, T. L, Fertig, J. E (2023). “Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces.” Cell Systems, 14(4). ISSN 2405-4712, doi:10.1016/j.cels.2023.03.004, https://www.cell.com/cell-systems/abstract/S2405-4712(23)00080-7.
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 | 1.2.1 |
| 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, jsonlite, Matrix, qvalue, stats, utils, methods |
| System Requirements | |
| URL | https://github.com/DeshpandeLab/SpaceMarkers |
| Bug Reports | https://github.com/DeshpandeLab/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 | 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.
| Source Package | SpaceMarkers_1.2.1.tar.gz |
| Windows Binary (x86_64) | SpaceMarkers_1.2.1.zip |
| macOS Binary (x86_64) | SpaceMarkers_1.2.1.tgz |
| macOS Binary (arm64) | SpaceMarkers_1.2.1.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 |
| Old Source Packages for BioC 3.20 | Source Archive |