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Bioconductor - Banksy

Banksy

This is the released version of Banksy; for the devel version, see Banksy.

Spatial transcriptomic clustering

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-4983-4714

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

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

To install this package, start R (version "4.5") and enter:


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

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 1.4.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) 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.

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