Skill Claude CodeCodex
Load when calling CNV segments via CBS-style segmentation on a bin-level log2-ratio CSV from exome / WGS coverage — emits per-segment 5-class CN state (amplification / gain / neutral / loss / deepdeletion), per-chromosome summary, genome-fraction-altered. Skip when working with single-cell / spatial CNV (use…
Skill Claude CodeCodex
Load when summarising a peak file (BED / narrowPeak) from ATAC-seq / ChIP-seq / CUT&Tag — peak count, width distribution, per-chromosome counts, score statistics. Skip when calling peaks from BAM (run MACS / Genrich externally first); working with single-cell ATAC (use scatac-preprocessing).
Skill Claude CodeCodex
Load when summarising a phased VCF (output of WhatsHap / SHAPEIT5 / Eagle2) — phased fraction of het variants, phase-block N50, PS-field parsing, pipe-delimited genotype detection. Skip when the input is unphased (run a phaser first); calling small variants (use genomics-variant-calling).
Skill Claude CodeCodex
Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection. Skip when working with already-aligned BAMs (use genomics-alignment); peak / variant files are the input (use the relevant downstream skill).
Skill Claude CodeCodex
Load when summarising structural variants from an SV VCF (DEL / DUP / INV / TRA) — BND-notation parsing, size classification, per-type counts. Skip when working with small SNVs / indels (use genomics-variant-calling); calling SVs from BAM (run Manta / Delly / Sniffles first).
Skill Claude CodeCodex
Load when summarising functional impact of an annotated variant CSV — per-IMPACT counts (HIGH / MODERATE / LOW / MODIFIER), top consequences, gene-affected count. Skip when input is a raw VCF (convert with bcftools +split-vep first); calling raw variants (use genomics-variant-calling); filtering VCFs (use…
Skill Claude CodeCodex
Load when summarising small variants (SNVs / indels) from a VCF or computing demo-pattern variant statistics (Ti/Tv ratio, per-chromosome distribution, SNP / indel split). Skip when filtering / merging VCFs (use genomics-vcf-operations); calling structural variants (use genomics-sv-detection); adding functional…
Skill Claude CodeCodex
Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing. Skip when the input is a BAM (use genomics-variant-calling); adding functional annotations (use genomics-variant-annotation).
Skill Claude CodeCodex
Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Skip when the dataset is already in hand; only routing a query (use orchestrator).
Skill Claude CodeCodex
Load when annotating LC-MS features against a built-in 15-metabolite HMDB demo dictionary by m/z within a --ppm tolerance — emits a per-feature annotation table. Skip when needing real HMDB / KEGG / LipidMaps / METLIN look-up (this skill is demo-only); raw spectra (use metabolomics-xcms-preprocessing).
Skill Claude CodeCodex
Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using --group-a-prefix / --group-b-prefix (default ctrl / treat). Skip when needing tunable test backends (use metabolomics-statistics); raw spectra.
Skill Claude CodeCodex
Load when normalising a feature × sample metabolomics CSV via median, quantile, total (sum), PQN (probabilistic quotient), or log methods — emits a normalised wide-form table. Skip when also imputing (use metabolomics-quantification); raw spectra (use metabolomics-xcms-preprocessing).