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Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome structure.
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.
QIIME2 microbiome analysis skill for 16S rRNA profiling and diversity analysis
Turns a shotgun profiler table (MetaPhlAn relative abundance, Bracken counts, HUMAnN function tables) into honest figures and defensible community statistics with phyloseq, vegan, microViz, and Python. Covers why an ordination/bar/diversity number is a modeling choice that can manufacture a resul...
Alpha and beta diversity of an amplicon (16S/ITS) ASV/OTU community table - observed features, Shannon, Pielou evenness, Faith PD, Bray-Curtis, Jaccard, weighted/unweighted/generalized UniFrac, Aitchison/RPCA - via QIIME2 core-metrics-phylogenetic, phyloseq/vegan, and scikit-bio. Covers the three...
End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy assignment, a SEPP/Greengenes2 tree, alpha/b...
Agent skill for Researcher, Data Scientist, published by GPTomics. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by majiayu000. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by majiayu000. Project details and file access are provided by the publisher.
Agent skill for Data Scientist, Researcher, Business Intelligence Analyst, published by Rudson-Oliveira. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by Rudson-Oliveira. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by Rudson-Oliveira. Project details and file access are provided by the publisher.
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