Subread — high-performance read alignment and quantification package using a seed-and-vote mapping strategy. Includes subread-align for genomic DNA and RNA-seq read alignment, subjunc for exon-junctio
Use with AI
Install the MCP server or CLI to instantly fetch Subread documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/subread
Benchmark and compare bioinformatics tools for a given analysis task using published benchmark data (accuracy, runtime, memory), PrecisionFDA and CAMI challenge results, bc7score community metrics, an
1 shared topic • 2 shared operations
PyDESeq2 — Python implementation of DESeq2 for differential gene expression analysis from bulk RNA-seq count data. Performs size factor normalization, genewise dispersion estimation, Wald tests with B
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
sleuth — R package for differential expression analysis of RNA-seq data at the transcript level. Works with kallisto bootstrap quantifications to model technical variability using a response error mod
1 shared topic • 2 shared operations