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Pegasus is a Python package for analyzing and visualizing large-scale single-cell and single-nucleus RNA-seq data, developed by the Broad Institute's Li Lab. Performs QC filtering, normalization, PCA,
Use with AI
Install the MCP server or CLI to instantly fetch Pegasus (Cumulus/Pegasus) documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/cumuluspegasus
Use when working with OneK1K tools from the Powell Genomics Lab — the single-cell eQTL (sc-eQTL) analysis suite built around the OneK1K cohort (~1.27 million PBMCs from 982 donors). Covers the full pi
3 shared topics • 2 shared operations
CellBender removes ambient RNA contamination and technical noise from droplet-based single-cell RNA-seq data using a deep generative model (VAE). Processes raw 10x Genomics feature-barcode matrices to
3 shared topics • 1 shared operation
CopyKAT (Copy number Karyotyping of Tumors) — R package for inferring genome-wide aneuploidy and copy number variations from single-cell RNA-seq data. Uses Bayesian segmentation to distinguish tumor (
3 shared topics • 1 shared operation
WARP (WDL Analysis Research Pipelines) — Broad Institute's cloud-optimized collection of genomics pipelines written in WDL (Workflow Description Language). Covers whole-genome sequencing (WGS), whole-
3 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
3 shared topics • 1 shared operation