Package: Banksy 1.3.0
Joseph Lee
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 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.
Authors:
Banksy_1.3.0.tar.gz
Banksy_1.3.0.zip(r-4.5)Banksy_1.3.0.zip(r-4.4)
Banksy_1.3.0.tgz(r-4.4-any)
Banksy_1.3.0.tar.gz(r-4.5-noble)Banksy_1.3.0.tar.gz(r-4.4-noble)
Banksy_1.3.0.tgz(r-4.4-emscripten)
Banksy.pdf |Banksy.html✨
Banksy/json (API)
NEWS
| # Install 'Banksy' in R: |
| install.packages('Banksy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/prabhakarlab/banksy/issues
- hippocampus - Mouse Hippocampus VeraFISH data
- rings - An unrealistic simulation of spatially-resolved omics data.
On BioConductor:Banksy-1.3.0(bioc 3.21)Banksy-1.2.0(bioc 3.20)
clusteringspatialsinglecellgeneexpressiondimensionreductionclustering-algorithmsingle-cell-omicsspatial-omics
Last updated 2 months agofrom:abf32654bc. Checks:OK: 1 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
Exports:clusterBanksyclusterNamescompareClusterscomputeBanksyconnectClustersgetBanksyMatrixrunBanksyPCArunBanksyUMAPsimulateDatasetsmoothLabels
Dependencies:abindaricodeaskpassBHBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicolorspacecpp11crayoncurldata.tableDBIdbplyrdbscanDelayedArraydplyrdqrngfansifarverfastmapfilelockFNNgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehttrigraphIRangesirlbaisobandjsonlitelabelinglatticeleidenAlglifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimemunsellnlmeopensslpbmcapplypillarpkgconfigplogrplyrpROCpurrrR6RColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHungarianRcppProgressrjsonrlangRSpectraRSQLiteS4ArraysS4VectorsscalessccoreSingleCellExperimentsitmoSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8uwotvctrsviridisLitewithrXVectorzlibbioc
Domain segmentation (STARmap PLUS mouse brain)
Rendered fromdomain-segment.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-01-03
Started: 2023-08-29
Multi-sample analysis (10x Visium Human DLPFC)
Rendered frommulti-sample.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-04-09
Started: 2023-07-25
Parameter selection (VeraFISH Mouse Hippocampus)
Rendered fromparameter-selection.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-03-08
Started: 2023-07-25
Spatial data integration with Harmony (10x Visium Human DLPFC)
Rendered frombatch-correction.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-04-09
Started: 2023-08-30
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Perform clustering in BANKSY's neighborhood-augmented feature space. | clusterBanksy |
| Get names of clustering runs. | clusterNames |
| Compare cluster outputs based on various clustering comparison measures. | compareClusters |
| Compute the component neighborhood matrices for the BANKSY matrix. | computeBanksy |
| Relabel cluster labels across parameter runs to maximise their similarity. | connectClusters |
| Builds the BANKSY matrix from neighborhood matrices. | getBanksyMatrix |
| Mouse Hippocampus VeraFISH data | hippocampus |
| An unrealistic simulation of spatially-resolved omics data. | rings |
| Run PCA on a BANKSY matrix. | runBanksyPCA |
| Run UMAP on a BANKSY embedding. | runBanksyUMAP |
| Simulate an unrealistic spatial omics dataset. | simulateDataset |
| k-Nearest neighbor cluster label smoothing. | smoothLabels |
