CytoML

CellPhoneDB — repository of curated receptors, ligands, and their interactions for cell-cell communication analysis from single-cell RNA-seq data. Performs permutation-based statistical analysis (stat

2 shared topics • 2 shared operations

DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

2 shared topics • 2 shared operations

Palantir — pseudotime and cell fate probability analysis for single-cell RNA-seq data using Markov diffusion chains. Computes a continuous pseudotime ordering from a user-specified start cell and quan

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