Niche

LIANA (LIgand-receptor ANAlysis) — unified Python framework for cell-cell communication inference from single-cell transcriptomics. Wraps multiple methods (CellPhoneDB, NATMI, Connectome, SingleCellSi

2 shared topics • 1 shared operation

NicheNet — R-based computational framework for studying intercellular communication from single-cell transcriptomics. Predicts which ligands expressed by sender cell types regulate target gene express

2 shared topics • 1 shared operation

scArches (Single-cell Architecture Surgery) — Python toolkit for reference-based single-cell data integration via transfer learning. Maps query datasets into pre-trained reference atlases using archit

2 shared topics • 1 shared operation

scFoundation — large-scale pretrained foundation model for single-cell transcriptomics built on the xTrimo transformer architecture. Trained on ~50 million human single-cell profiles, scFoundation gen

2 shared topics • 1 shared operation

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 • 1 shared operation