Loading homepage
densMAP — density-preserving dimensionality reduction for visualization. Augments UMAP with a density-correlation regularizer that preserves local density information from high-dimensional data in the
Use with AI
Install the MCP server or CLI to instantly fetch densMAP documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/densmap
10x Genomics — commercial platform for single-cell and spatial genomics assays including Chromium single-cell RNA-seq (scRNA-seq), single-cell ATAC-seq, single-cell multiome (RNA+ATAC), Visium spatial
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
2 shared topics • 1 shared operation
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
2 shared topics • 1 shared operation
DoRothEA — Discriminant Regulon Expression Analysis R/Bioconductor package for transcription factor (TF) activity inference from gene expression data. Provides curated TF regulons (confidence levels A
2 shared topics • 1 shared operation
scater — Bioconductor single-cell RNA-seq QC and visualization toolkit built on SingleCellExperiment. Use when user needs per-cell QC metrics with addPerCellQCMetrics, adaptive MAD-based outlier detec
2 shared topics • 1 shared operation