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GiottoUtils - Giotto Suite Utilities

Utility functions and imports for Giotto Suite.

Last updated

softwaretechnologyspatial

3.95 score 3 stars 6 scripts

smotifrs - Rust backend for smotif motif enumeration

Drop-in Rust acceleration for the smotif R package: parallel enumeration of size-2 / size-3 / size-4 multi-cellular motifs in spatial omics graphs, plus direct parquet I/O for million-cell datasets. Distributed as pre-compiled binaries via R-universe.

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rustcargo

2.70 score 3 scripts

smotif - Spatial Multi-Cellular Motifs

Discovery and statistical evaluation of recurrent multi-cellular motifs (size 2, 3, and 4) in spatial omics data. Provides a lightweight 'SpatialGraph' representation backed by parquet, enumeration over igraph, spatially-aware null models, motif-to-gene association, and cross-region or cross-sample comparison. Designed to be framework-agnostic so that the core can be folded into Giotto Suite later.

Last updated

2.70 score 4 scripts

spatialDWLS - Cell Type Deconvolution of Spatial Transcriptomics with Dampened Weighted Least Squares

Estimates the cell type composition of each spot of a spatial transcriptomics experiment from a single-cell reference, following spatialDWLS (Dong and Yuan 2021, <doi:10.1186/s13059-021-02362-7>), which builds on dampened weighted least squares (DWLS; Tsoucas et al. 2019, <doi:10.1038/s41467-019-10802-z>). Spots are solved in two rounds: candidate cell types are chosen per cluster by enrichment, then each spot is re-solved against the types present in it. Works on dense or sparse matrices, in parallel through 'BiocParallel', and over windows of spots for expression stores that do not fit in memory.

Last updated

2.70 score 4 scripts