SpiecEasi

Use when working with microeco — an R6-class R package for microbiome community ecology analysis. Handles OTU/ASV tables, taxonomy, sample metadata, and phylogenetic trees in a unified microtable obje

2 shared topics • 2 shared operations

NetCoMi (Network Construction and Comparison for Microbiome Data) — R package for constructing, analyzing, and comparing microbial association and dissimilarity networks from compositional count data.

2 shared topics • 1 shared operation

CellChat — R package for inference, analysis, and visualization of cell-cell communication networks from single-cell RNA-seq data. Uses a curated ligand-receptor database (CellChatDB) to quantify sign

1 shared topic • 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

1 shared topic • 2 shared operations

geNomad — identify viruses and plasmids in metagenomic assemblies and isolate genomes using neural-network sequence embeddings and marker gene profiles. Classifies sequences as chromosome, plasmid, or

2 shared topics