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Harmony -- fast and scalable single-cell data integration and batch correction algorithm. Operates on PCA embeddings using iterative soft k-means clustering to remove batch effects while preserving bi
Use with AI
Install the MCP server or CLI to instantly fetch Harmony -- Single-Cell Data Integration documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/harmony
Cellranger-arc — 10x Genomics pipeline for processing Multiome ATAC + Gene Expression data from the Chromium Multiome kit. Aligns FASTQ reads, calls peaks, quantifies gene expression and chromatin acc
1 shared topic • 2 shared operations
GLUE (Graph-Linked Unified Embedding) — deep learning framework for integrating unpaired single-cell multi-omics data (scRNA-seq, scATAC-seq, snmC-seq). Uses a guidance graph of prior regulatory inter
1 shared topic • 2 shared operations
Use when working with SAMap for cross-species single-cell RNA-seq atlas alignment, manifold mapping, homolog graph construction, or cell-type conservation analysis. SAMap maps AnnData or SAM objects a
1 shared topic • 2 shared operations
Spectre is an R toolkit for high-dimensional single-cell cytometry and imaging analysis, including data import (CSV/FCS), metadata integration, arcsinh/logicle transformation, clustering (FlowSOM, Phe
1 shared topic • 2 shared operations
STARmap (Spatially-resolved Transcript Amplicon Readout mapping) — in situ spatial transcriptomics method that combines hydrogel-tissue chemistry with sequencing-by-hybridization (SEDAL) for multiplex
1 shared topic • 2 shared operations