Skill Claude CodeCodex
Access UniProt protein database for sequences, annotations, and functional information. Use when retrieving protein data, GO terms, domain annotations, or protein-protein interactions.
Skill Claude CodeCodex
Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.
Skill Claude CodeCodex
Calculates species richness, diversity, and turnover using the Hill number framework with iNEXT coverage-based rarefaction/extrapolation, asymptotic diversity estimation, and beta diversity partitioning (betapart turnover vs nestedness). Compares assemblages using coverage-standardized rather than size-standardized…
Skill Claude CodeCodex
Analyzes community composition using constrained ordination (CCA, RDA, db-RDA), variance partitioning (varpart), indicator species analysis (indicspecies multipatt), and distance-based environmental gradient methods with vegan. Links species composition to environmental explanatory variables. Use when testing how…
Skill Claude CodeCodex
Assesses genetic health of populations for conservation using effective population size estimation (GONE2 for recent Ne trajectory, NeEstimator for contemporary Ne, Stairway Plot 2 and PSMC for historical Ne), F-statistics (hierfstat), runs of homozygosity (detectRUNS), and genetic diversity metrics. Use when…
Skill Claude CodeCodex
Processes environmental DNA metabarcoding data from raw amplicon reads to species occurrence tables using OBITools3, DADA2, and taxonomic assignment against BOLD, MIDORI2, or MitoFish databases. Handles COI, 12S, rbcL, and ITS barcode regions with primer removal, denoising, chimera detection, and contamination…
Skill Claude CodeCodex
Tests genotype-environment associations and identifies loci under local adaptation using LFMM2 (LEA), pcadapt outlier detection, OutFLANK Fst-based selection scans, and redundancy analysis. Detects adaptive genetic variation correlated with environmental variables while controlling for population structure. Use when…
Skill Claude CodeCodex
Delimits species boundaries from molecular data using distance-based (ASAP), tree-based (bPTP, GMYC), and coalescent (BPP) methods. Compares multiple delimitation results with delimtools. Use when delineating putative species from DNA barcoding data, resolving cryptic species complexes, or validating taxonomic…
Skill Claude CodeCodex
Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.
Skill Claude CodeCodex
Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.
Skill Claude CodeCodex
Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states. Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees.
Skill Claude CodeCodex
Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders.