SPARK

Use when working with Conos (Clustering On Network Of Samples), the R package for joint analysis of multiple single-cell RNA-seq and spatial transcriptomics datasets. Covers building joint k-nearest-n

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

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

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