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Use when working with scran pooling normalization — scranpool — the pool-and-deconvolve size-factor estimation method for single-cell RNA-seq normalization. Pools cells to robustly estimate size facto
Use with AI
Install the MCP server or CLI to instantly fetch SCRAN.pool documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/scranpool
scHPF — single-cell Hierarchical Poisson Factorization for de novo gene program discovery in scRNA-seq data. Decomposes raw UMI count matrices into interpretable cell scores (theta) and gene loadings
2 shared topics • 2 shared operations
Use this skill for SCTransform normalization of single-cell RNA-seq count matrices. Route here when users ask about variance stabilizing transformation (VST), regularized negative binomial regression
2 shared topics • 2 shared operations
CytoTRACE -- computational method for predicting relative differentiation state of cells from single-cell RNA-seq data. Uses gene counts (number of detectably expressed genes per cell) as a robust pro
2 shared topics • 1 shared operation
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
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