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nf-core/rnaseq — production Nextflow pipeline for bulk RNA-seq analysis including read QC, trimming, alignment (STAR/HISAT2), pseudo-alignment (Salmon), quantification, and comprehensive quality contr
Use with AI
Install the MCP server or CLI to instantly fetch nf-corernaseq documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/nf-corernaseq
alevin-fry — fast, accurate, and memory-frugal Rust-based tool for single-cell and single-nucleus RNA-seq quantification. Processes RAD (Reduced Alignment Data) files from salmon alevin to generate ce
1 shared topic • 2 shared operations
RASQUAL (Robust Allele Specific QUantification and quality controL) — joint QTL mapping tool that integrates total read counts and allele-specific reads for cis-regulatory variant discovery. Detects i
1 shared topic • 2 shared operations
RNA-SeQC — fast C++ tool for RNA-seq quality control and gene-level quantification for large cohorts. Computes 70+ QC metrics including alignment rates, rRNA contamination, GC bias, 3'/5' coverage bia
1 shared topic • 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
1 shared topic • 2 shared operations
Salmon is an ultrafast, bias-correcting tool for quantifying transcript abundances from RNA-seq reads using quasi-mapping or selective alignment. Alevin is Salmon's single-cell mode for generating cel
1 shared topic • 2 shared operations