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- 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.Learn more: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.bioconductor.org/packages/release/bioc/manuals/B…BANKSY encodes the microenvironment of a cell using a pair of spatial kernels: one constructed using the weighted mean of gene expression in each cell’s neighbourhood, and the other using an azimuthal Gabor filter.www.nature.com/articles/s41576-024-00743-9
BANKSY unifies cell typing and tissue domain segmentation for …
Feb 27, 2024 · BANKSY labels spatially structured cell types and subtypes with high accuracy and is adept at distinguishing subtly different cell subtypes residing in distinct microenvironments.
BANKSY: scalable cell typing and domain segmentation for
May 15, 2024 · We demonstrated spatially aware batch correction by applying the existing batch correction tool Harmony directly to the embedding produced by BANKSY to integrate 12 …
BANKSY unifies cell typing and tissue domain segmentation for …
BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can also …
highly versatile, with its utility extending beyond cell typing and domain segmentation. We demonstrated spatially aware batch cor-rection by applying the existing batch correction tool …
prabhakarlab/Banksy: Spatial transcriptomic clustering
Jul 31, 2024 · 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 …
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 …
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Banksy: Spatial transcriptomic clustering
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 …
satijalab/seurat-wrappers: docs/banksy.md - R Package …
Nov 23, 2024 · BANKSY is a method that incorporates neighborhood information for clustering spatial omics data. By doing so, BANKSY is able to improve cell-type assignment in noisy data
Banksy - Bioconductor
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 …
BANKSY unifies cell typing and tissue domain segmentation for …
Jan 22, 2025 · BANKSY can also be used for quality control of spatial transcriptomics data and for spatially aware batch effect correction. Importantly, it is substantially faster and more scalable …
(PDF) BANKSY: A Spatial Omics Algorithm that …
Apr 15, 2022 · BANKSY’s spatial kernel-based feature augmentation strategy improves per-formance and scalability on both tasks when tested on FISH-based and sequencing-based spatial omics data....
Banksy-package : The Banksy package - R Package Documentation
Jul 31, 2024 · 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 …
seurat-wrappers/docs/banksy.Rmd at master - GitHub
With low values of lambda, BANKSY operates in cell-typing mode, while high values of lambda find spatial domains. - `assay` and `slot`: determines where to pull the expression data from - …
BANKSY unifies cell typing and tissue domain segmentation
BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can also …
BANKSY: scalable cell typing and domain segmentation for
May 15, 2024 · BANKSY’s spatial feature augmentation strategy improved performance on both tasks when tested on diverse RNA (imaging, sequencing) and protein (imaging) datasets.
10 Clustering – Orchestrating Spatial Transcriptomics Analysis …
Alternatively, we can use spatially-aware clustering algorithms that directly take the spatial coordinates of the measurements into account. For larger datasets, there may also be …
satijalab/seurat-wrappers: docs/banksy.Rmd - R Package …
Nov 23, 2024 · Compute a spatially-aware embedding with PCA on the BANKSY matrix, and run Harmony on this embedding.
Tissue module discovery in single-cell-resolution spatial ...
Jun 19, 2024 · For BANKSY, while it identified the upper-layer astrocyte subtypes with a similar spatially distributed pattern as SPACE, it mixed the astrocytes in the deep-layer and in the …
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