Banksy
This is the development version of Banksy; for the stable release version, see Banksy.
Spatial transcriptomic clustering
Bioconductor version: Development (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:
Maintainer: Joseph Lee <joseph.lee at u.nus.edu>
citation("Banksy")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DimensionReduction, GeneExpression, SingleCell, Software, Spatial |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |