SpaceMarkers
This is the released version of SpaceMarkers; for the devel version, see SpaceMarkers.
Spatial Interaction Markers
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.2.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| 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, 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, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap |
| 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_2.2.0.tar.gz |
| Windows Binary (x86_64) | SpaceMarkers_2.2.0.zip |
| macOS Binary (big-sur-x86_64) | SpaceMarkers_2.2.0.tgz |
| macOS Binary (sonoma-arm64) | SpaceMarkers_2.2.0.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 |