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Use when working with EmptyDrops or DropletUtils — the Bioconductor R package for distinguishing real cells from empty droplets in droplet-based single-cell RNA-seq data (10x Genomics, Drop-seq, inDro
Use with AI
Install the MCP server or CLI to instantly fetch EmptyDrops (DropletUtils) documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/emptydrops
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
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
3 shared topics • 1 shared operation
Human Cell Atlas (HCA) tools — programmatic access to the HCA Data Portal, Data Coordination Platform (DCP), and matrix service for single-cell genomics datasets. Covers the hca Python CLI client, Azu
3 shared topics • 1 shared operation
Use when performing single-cell QTL (sc-eQTL, sc-sQTL) mapping with SAIGE-QTL. SAIGE-QTL extends the SAIGE framework to single-cell RNA-seq data using Poisson mixed models to handle count overdispersi
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