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UMAP (Uniform Manifold Approximation and Projection) — nonlinear dimensionality reduction for visualization and general-purpose embedding. Constructs fuzzy simplicial complex from high-dimensional dat
Use with AI
Install the MCP server or CLI to instantly fetch UMAP documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/umap-learn
ConsensusClusterPlus — R/Bioconductor package for determining cluster count and membership by stability evidence in unsupervised analysis, implementing the Monti et al. (2003) consensus clustering alg
1 shared topic • 2 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
iheatmapr — rOpenSci R package for building interactive, multi-panel complex heatmaps powered by plotly. Constructs modular iheatmap S4 objects by chaining add_* functions: add_col_signal, add_row_sig
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