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Pavian — interactive R/Shiny web application for metagenomics analysis and visualization. Reads classification reports from Kraken, Kraken2, Bracken, MetaPhlAn, DIAMOND+MEGAN, and Centrifuge to genera
Use with AI
Install the MCP server or CLI to instantly fetch Pavian documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/pavian
docker pull biocontainers/pavian:1.0phyloseq -- R/Bioconductor package for importing, storing, analyzing, and visualizing microbiome census data. Handles OTU/ASV tables, taxonomy tables, sample metadata, phylogenetic trees, and referenc
2 shared topics • 2 shared operations
CNVkit -- Python toolkit for detecting copy number variants (CNVs) from targeted DNA sequencing data (hybrid capture, amplicon) and whole-genome sequencing (WGS). Leverages both on-target and off-targ
2 shared topics • 1 shared operation
CRISPR-DAV (CRISPR DNA Analysis and Visualization) is a pipeline for analyzing and visualizing CRISPR editing outcomes from amplicon sequencing (NGS) data. Detects indels, substitutions, HDR events, a
2 shared topics • 1 shared operation
DADA2 — high-resolution amplicon sequence variant (ASV) inference from Illumina, 454, and Ion Torrent amplicon sequencing data. R/Bioconductor package that models sequencing errors to resolve exact bi
2 shared topics • 1 shared operation
VSEARCH — open-source, multithreaded alternative to USEARCH for amplicon and metagenomics sequence analysis. Performs dereplication, chimera detection (de novo and reference-based), OTU/ASV clustering
2 shared topics • 1 shared operation