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
Use with AI
Install the MCP server or CLI to instantly fetch Cellranger-arc documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/cellranger-arc
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 • 2 shared operations
FLAMES — Full-Length Analysis of Mutations and Splicing for bulk and single-cell long-read RNA-seq data. R/Bioconductor pipeline for barcode demultiplexing, isoform discovery, transcript quantificatio
3 shared topics • 2 shared operations
nf-core/scrnaseq — Nextflow pipeline for single-cell RNA-seq quantification and preprocessing. Supports multiple alignment/quantification methods including Cell Ranger, STARsolo, Alevin-fry (Salmon),
3 shared topics • 2 shared operations
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 • 2 shared operations
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 • 2 shared operations