Battlefield
Swiss-army toolkit for selecting niche fronts and invasive margins in spatial transcriptomics data
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Battlefield is a Swiss-army toolkit originally developed to define and extract spatial spots from specific tissue regions—such as front regions, niche borders, invasive margins, and cluster interfaces—using spatial transcriptomics data or clustered tissue maps. It has since been extended to support trajectory selection and layer inspection, and now provides a collection of low-level utilities for spatial transcriptomics analysis. These utilities are primarily intended to be reused within higher-level analytical packages. It is designed to work with sequencing-based platforms such as Visium at several resolutions and Visium HD(binned).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Battlefield")Details
| Maintainer | Jean-Philippe Villemin <jpvillemin@gmail.com> |
| Author | Jean-Philippe Villemin [aut, cre] (ORCID: <https://orcid.org/0000-0002-1838-5880>), European Research Council [fnd] (ERC-2022) |
| License | CeCILL | file LICENSE |
| URL | https://github.com/ZheFrench/BattleField, https://zhefrench.github.io/Battlefield/ |
| Bug Reports | https://github.com/ZheFrench/BattleField/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Sequencing, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/Battlefield/ |
Citation
From within R, enter citation("Battlefield"):
Jean-Philippe Villemin. Battlefield: Swiss-army toolkit for selecting niche fronts and invasive margins in spatial transcriptomics data. doi:10.18129/B9.bioc.Battlefield, R package version 1.0.0, https://bioconductor.org/packages/Battlefield.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | Battlefield_1.0.0.tar.gz |
| Windows binary (x86_64) | Battlefield_1.0.0.zip |
| macOS binary (arm64) | Battlefield_1.0.0.tgz |
| macOS binary (x86_64) | Battlefield_1.0.0.tgz |
Dependencies
Depends: R (>= 4.5)
Imports: stats, RANN, dplyr, SummarizedExperiment, methods
Suggests: BiocStyle, knitr, markdown, rmarkdown, SpatialExperiment, SpatialExperimentIO, VisiumIO, ggplot2, pheatmap, pals, OSTA.data, tidyr, STexampleData, testthat (>= 3.0.0), codetools, grid, tools