Perform biological sequence analysis and microbiome ecology workflows with scikit-bio.
npx skills add https://github.com/shushuzn/Rairos --skill scikit-bio-shushuzn
Please help me install this Agent Skill. Skill: scikit-bio Source: https://github.com/shushuzn/Rairos/tree/main/skills/scikit-bio Command: npx skills add https://github.com/shushuzn/Rairos --skill scikit-bio-shushuzn
It helps you analyze biological sequences and microbiome/community data end-to-end—covering file I/O, alignments, phylogenetics, diversity metrics, ordination, and key non-parametric tests—without stitching together multiple fragile tools.
Use the scikit-bio skill to compute PCoA coordinates from your beta-diversity distance matrix and report the main axes for your sample groups.
High-intent search queries and answers about installing and using this skill.
To calculate UniFrac beta diversity distances, you load your BIOM feature table and matching Newick tree, ensuring OTU/ASV identifiers map correctly between them, then compute the distance matrix using scikit-bio's diversity functions for downstream ordination.
Yes, you can run permutation-based tests like PERMANOVA and Mantel directly on a distance matrix using scikit-bio, which validates group differences and correlations within microbial community ecology workflows without requiring external statistical packages.
You run PCoA ordination on beta-diversity distance matrices by passing the computed distance matrix into scikit-bio's ordination functions, generating principal coordinates that visualize sample groupings for downstream statistical reporting.
Yes, scikit-bio supports reading and writing common biological formats including FASTA, FASTQ, and GenBank, allowing validated sequence manipulations like reverse complement, transcription, and translation directly within the Python environment.
The best way to align sequences and build phylogenetic trees is using scikit-bio's pairwise and multiple alignment functions, then constructing trees from the resulting distance matrices while evaluating topology comparisons.
Ordination fails when OTU or ASV identifiers mismatch between BIOM tables and phylogenetic trees because scikit-bio requires correct identifier mapping to generate distance-matrix-compatible inputs for downstream diversity calculations and statistical tests.
pur3v4d3rAnalyze biological sequences and phylogenetic data with scikit-bio.
LeonChaoXAnalyze biological sequences and microbiome ecology with scikit-bio.
galeepPerform bioinformatics sequence manipulation, alignment, and diversity analysis with scikit-bio.
Estrella-231Compute diversity, ordination, and statistical summaries from sequence-derived inputs.
