scFoundation

CellGenIT tools from the Wellcome Sanger Institute Cellular Genetics Informatics team. Suite of Python utilities for single-cell genomics including sinto (fragment file generation from BAM), cellhint

2 shared topics • 1 shared operation

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

STdeconvolve — reference-free cell-type deconvolution for spatial transcriptomics using Latent Dirichlet Allocation (LDA). Decomposes multi-cellular spatial pixels into cell-type proportions and trans

2 shared topics • 1 shared operation