NicheNet

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 • 2 shared operations

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 • 2 shared operations

pySCENIC — Python implementation of SCENIC for single-cell gene regulatory network inference and regulon analysis. Implements a three-step pipeline: GRN inference via GRNBoost2 or GENIE3, cis-regulato

2 shared topics • 2 shared operations

SCENIC (pySCENIC) — gene regulatory network inference and transcription factor regulon analysis for single-cell RNA-seq data. Infers TF-target gene networks using GRNBoost2/GENIE3, refines regulons vi

2 shared topics • 2 shared operations

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 • 2 shared operations