Browse reusable Agent Skills, each with a clear purpose and practical guidance.
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.
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.
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis. Use when performing supervised multi-omics integration or identifying features that discriminate between groups.
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation. Use when integrating RNA-seq, proteomics, methylation, or other omics to discover latent factors driving biological variation across modalities.
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network. Use when performing patient stratification or integrating multi-omics data into unified similarity networks.
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone to microbial contamination.
Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use when identifying translated regions beyond annotated coding sequences or quantifying ORF-level translation.
Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon-specific translation dynamics.
Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.