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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
Use with AI
Install the MCP server or CLI to instantly fetch SAMap documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/samap
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
2 shared topics • 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
2 shared topics • 1 shared operation
estimate-compute-requirements — predict CPU, memory, wall time, and storage for bioinformatics pipelines given input data size and tool selection. Generates per-step resource tables, platform-specific
2 shared topics • 1 shared operation
salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s
2 shared topics • 1 shared operation
Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering
2 shared topics • 1 shared operation