ConsensusClusterPlus

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

1 shared topic • 3 shared operations

Cumulus — cloud-based framework for large-scale single-cell and single-nucleus RNA-seq analysis on Terra/Google Cloud. Provides WDL workflows for demultiplexing (demuxEM, souporcell, demuxlet), count

1 shared topic • 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

1 shared topic • 2 shared operations

MetaCell is the original Tanay lab R package for building metacells from single-cell RNA-seq UMI matrices by partitioning a balanced cell similarity graph into small homogeneous groups. Use it for 10x

1 shared topic • 2 shared operations

stLearn — spatial transcriptomics analysis in Python integrating gene expression with tissue morphology. Provides SME (spatial morphological gene expression) normalization, spatial clustering, spatial

1 shared topic • 2 shared operations