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Banksy

This is the development version of Banksy; to use it, please install the devel version of Bioconductor.

Spatial transcriptomic clustering


Bioconductor version: Development (3.19)

Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.

Author: Vipul Singhal [aut], Joseph Lee [aut, cre]

Maintainer: Joseph Lee <joseph.lee at u.nus.edu>

Citation (from within R, enter citation("Banksy")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Banksy")

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("Banksy")
Domain segmentation (STARmap PLUS mouse brain) HTML R Script
Multi-sample analysis (10x Visium Human DLPFC) HTML R Script
Parameter selection (VeraFISH Mouse Hippocampus) HTML R Script
Spatial data integration with Harmony (10x Visium Human DLPFC) HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, DimensionReduction, GeneExpression, SingleCell, Software, Spatial
Version 0.99.12
In Bioconductor since BioC 3.19 (R-4.4)
License file LICENSE
Depends R (>= 4.4.0)
Imports aricode, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, matrixStats, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian
System Requirements
URL https://github.com/prabhakarlab/Banksy
Bug Reports https://github.com/prabhakarlab/Banksy/issues
See More
Suggests knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle
Linking To
Enhances
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 Banksy_0.99.12.tar.gz
Windows Binary Banksy_0.99.12.zip
macOS Binary (x86_64) Banksy_0.99.12.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/Banksy
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Banksy
Bioc Package Browser https://code.bioconductor.org/browse/Banksy/
Package Short Url https://bioconductor.org/packages/Banksy/
Package Downloads Report Download Stats