Battlefield
This is the released version of Battlefield; for the devel version, see Battlefield.
Swiss-army toolkit for selecting niche fronts and invasive margins in spatial transcriptomics data
Bioconductor version: Release (3.23)
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).
Author: Jean-Philippe Villemin [aut, cre] 
, European Research Council [fnd] (ERC-2022)
Maintainer: Jean-Philippe Villemin <jpvillemin at gmail.com>
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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Battlefield")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("Battlefield")| Battlefield-Main | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Sequencing, Software, Spatial, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | CeCILL | file LICENSE |
| Depends | R (>= 4.5) |
| Imports | stats, RANN, dplyr, SummarizedExperiment, methods |
| System Requirements | |
| URL | https://github.com/ZheFrench/BattleField https://zhefrench.github.io/Battlefield/ |
| Bug Reports | https://github.com/ZheFrench/BattleField/issues |
See More
| Suggests | BiocStyle, knitr, markdown, rmarkdown, SpatialExperiment, SpatialExperimentIO, VisiumIO, ggplot2, pheatmap, pals, OSTA.data, tidyr, STexampleData, testthat (>= 3.0.0), codetools, grid, tools |
| Linking To | |
| Enhances | |
| 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 | Battlefield_1.0.0.tar.gz |
| Windows Binary (x86_64) | Battlefield_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | Battlefield_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | Battlefield_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Battlefield |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Battlefield |
| Package Short Url | https://bioconductor.org/packages/Battlefield/ |
| Package Downloads Report | Download Stats |