BANKSY

Use when working with MENDER (MultilayEred NeighborhooDhood-Encoded Representations), a Python tool for spatial domain identification in multiplexed imaging data. Covers spatial domain segmentation in

2 shared topics • 2 shared operations

Squidpy — spatial single-cell analysis toolkit in the scverse ecosystem for analyzing and visualizing spatial molecular data. Builds spatial neighbor graphs from tissue coordinates (Visium, Xenium, ME

2 shared topics • 2 shared operations

STARmap (Spatially-resolved Transcript Amplicon Readout mapping) — in situ spatial transcriptomics method that combines hydrogel-tissue chemistry with sequencing-by-hybridization (SEDAL) for multiplex

2 shared topics • 2 shared operations

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

2 shared topics • 1 shared operation

stLearn — spatial transcriptomics analysis in Python integrating gene expression with tissue morphology. Provides SME (spatial morphological gene expression) normalization, spatial clustering, spatial

2 shared topics • 1 shared operation