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sva — R/Bioconductor package for surrogate variable analysis, batch effect correction, and unwanted variation removal in high-throughput experiments. Provides sva() for estimating surrogate variables,
Use with AI
Install the MCP server or CLI to instantly fetch sva documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/sva
Cufflinks — RNA-seq transcript assembly, quantification, and differential expression suite. Assembles aligned reads into transcripts (cufflinks), performs differential expression analysis at transcrip
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