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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),
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Install the MCP server or CLI to instantly fetch nf-corescrnaseq documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/nf-corescrnaseq
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 • 2 shared operations
Use when working with DropletUtils for processing droplet-based single-cell RNA-seq data from 10x Genomics CellRanger output. DropletUtils provides read10xCounts() for loading MEX/HDF5 output, emptyDr
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
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