goose-bio-skills

In the author's own words, from each skill's SKILL.md — showing the first 29 of 60 files.

• alignment-file-operations

  Inspect, sort, index, filter, convert or summarize existing SAM/BAM/CRAM alignments. Exclude read alignment, variant calling and biological interpretation.

  skills/alignment-file-operations/SKILL.md on GitHub (opens in a new tab)

• amplicon-alpha-diversity-analysis

  Calculate per-sample observed features, Shannon and Simpson alpha diversity from amplicon integer-count TSVs. Return not-estimable for zero depth; exclude normalization, beta diversity and group tests.

  skills/amplicon-alpha-diversity-analysis/SKILL.md on GitHub (opens in a new tab)

• amplicon-beta-diversity-distance-analysis

  Calculate Bray-Curtis or binary Jaccard sample distances from amplicon integer-count TSVs. Exclude normalization, ordination, PERMANOVA and biological interpretation.

  skills/amplicon-beta-diversity-distance-analysis/SKILL.md on GitHub (opens in a new tab)

• amplicon-feature-table-and-taxonomy-qc

  Check amplicon feature-count TSVs, sample metadata and optional taxonomy for structural consistency. Exclude filtering, diversity analysis, taxonomic assignment and contamination decisions.

  skills/amplicon-feature-table-and-taxonomy-qc/SKILL.md on GitHub (opens in a new tab)

• bioinformatics-format-and-identifier-validation

  Validate FASTA/FASTQ/GenBank, SAM/BAM/CRAM, VCF/BCF structure or NCBI/UniProt identifier syntax, with optional exact-accession existence checks. Exclude retrieval, remapping, conversion and format-specific biological interpretation.

  skills/bioinformatics-format-and-identifier-validation/SKILL.md on GitHub (opens in a new tab)

• bioinformatics-qc-and-publication-reporting

  Assemble local analysis outputs into a source-linked report and execution-methods record. Exclude: Invented results, automatic scientific certification, clinical advice, manuscript conclusions and analysis reruns.

  skills/bioinformatics-qc-and-publication-reporting/SKILL.md on GitHub (opens in a new tab)

• bioinformatics-result-visualization

  Export source-backed volcano, PCA, heatmap, group, correlation, concordance, marker or embedding figures. Exclude: Invented values, silent scale conversion, automatic feature fishing, biological conclusions and new statistical tests.

  skills/bioinformatics-result-visualization/SKILL.md on GitHub (opens in a new tab)

• biological-database-record-retrieval-and-identifier-resolution

  Resolve gene identifiers with a declared local mapping table or retrieve bounded public gene, transcript and protein records. Preserve ambiguous mappings and provenance; exclude remote bulk jobs, literature and clinical interpretation.

  skills/biological-database-record-retrieval-and-identifier-resolution/SKILL.md on GitHub (opens in a new tab)

• biomedical-literature-and-public-study-search

  Find biomedical publications and public study accessions from a research question. Exclude evidence synthesis, read downloads and clinical recommendations.

  skills/biomedical-literature-and-public-study-search/SKILL.md on GitHub (opens in a new tab)

• bulk-rnaseq-gene-count-matrix-assembly

  Assemble a gene-count matrix from completed compatible single-sample counting reports with the same annotation and assignment policy. Exclude read counting, normalization and differential expression.

  skills/bulk-rnaseq-gene-count-matrix-assembly/SKILL.md on GitHub (opens in a new tab)

• bulk-rnaseq-gene-counting-from-alignment

  Count primary single-end SAM alignments against a GTF with explicit strand and MAPQ policies. Exclude paired-end counting, transcript quantification and differential expression.

  skills/bulk-rnaseq-gene-counting-from-alignment/SKILL.md on GitHub (opens in a new tab)

• chemical-similarity-and-substructure-search

  Search chemical similarity or substructures with declared molecular representations and search settings. Exclude inferring activity, efficacy or safety from structural matches.

  skills/chemical-similarity-and-substructure-search/SKILL.md on GitHub (opens in a new tab)

• chromatin-peak-set-qc

  Check up to four same-build BED3 or narrowPeak sets with declared contig lengths and optional blacklist. Exclude peak calling, FRiP, IDR, consensus construction and biological interpretation.

  skills/chromatin-peak-set-qc/SKILL.md on GitHub (opens in a new tab)

• correlation-and-association-screening

  Screen explicitly selected Pearson or Spearman variable pairs with optional bounded permutation inference. Exclude: Automatic all-pairs mining, batch adjustment, repeated measures, partial correlation and causal inference.

  skills/correlation-and-association-screening/SKILL.md on GitHub (opens in a new tab)

• count-based-differential-expression

  Analyze raw count matrices and sample metadata for one declared differential-expression contrast. Use the bounded local DESeq2 adapter when compatible; exclude FASTQ processing, enrichment and cross-adapter parity claims.

  skills/count-based-differential-expression/SKILL.md on GitHub (opens in a new tab)

• distance-matrix-principal-coordinates-analysis

  Run classical PCoA on an existing complete sample distance matrix or native beta-diversity distances, retaining negative eigenvalues. Exclude abundance preprocessing, PCA, PERMANOVA and group inference.

  skills/distance-matrix-principal-coordinates-analysis/SKILL.md on GitHub (opens in a new tab)

• environment-and-provenance-capture

  Record, compare or verify a biological analysis environment and provenance manifest. Exclude installation, upgrades, pipeline execution and workflow authoring.

  skills/environment-and-provenance-capture/SKILL.md on GitHub (opens in a new tab)

• evidence-synthesis-and-research-traceability

  Synthesize an identified biomedical evidence corpus with claim-to-source traceability and uncertainty. Exclude primary literature discovery and clinical decision authority.

  skills/evidence-synthesis-and-research-traceability/SKILL.md on GitHub (opens in a new tab)

• experimental-design-power-and-batch-planning

  Plan sample size, power, allocation, randomization, blocking or confounding review for a biological study. Exclude wet-lab execution, invented effect sizes and claims that analysis repairs complete confounding.

  skills/experimental-design-power-and-batch-planning/SKILL.md on GitHub (opens in a new tab)

• fcs-file-io-and-metadata-qc

  Inspect FCS structure, channels and metadata before cytometry analysis. Exclude compensation, gating, cell classification and clinical interpretation.

  skills/fcs-file-io-and-metadata-qc/SKILL.md on GitHub (opens in a new tab)

• flow-cytometry-arcsinh-transformation

  Apply arcsinh to declared cytometry event columns using explicit positive cofactors. Exclude selecting cofactors, compensation, gating and cell classification.

  skills/flow-cytometry-arcsinh-transformation/SKILL.md on GitHub (opens in a new tab)

• flow-cytometry-compensation-application

  Apply a supplied spillover matrix to a compatible cytometry event TSV. Exclude estimating spillover, raw FCS parsing, gating and clinical interpretation.

  skills/flow-cytometry-compensation-application/SKILL.md on GitHub (opens in a new tab)

• genomic-interval-operations

  Merge or intersect same-build BED3 intervals with explicit coordinate, strand, duplicate and adjacency policies. Guide broader interval tasks only with a declared compatible tool; exclude liftover, peak calling and biological consensus claims.

  skills/genomic-interval-operations/SKILL.md on GitHub (opens in a new tab)

• gff-gtf-gene-model-qc

  Check a declared GFF/GTF gene model against explicit contig lengths and coordinate conventions. Exclude annotation repair, sequence retrieval and expression quantification.

  skills/gff-gtf-gene-model-qc/SKILL.md on GitHub (opens in a new tab)

• human-variant-evidence-retrieval

  Retrieve bounded ClinVar evidence for one to five exact Variation IDs or VCV accessions. Exclude allele search, RCV lookup, pathogenicity reassessment and clinical decisions.

  skills/human-variant-evidence-retrieval/SKILL.md on GitHub (opens in a new tab)

• independent-2x2-categorical-comparison

  Compare one independent 2x2 integer count table with a two-sided Fisher exact test and conditional odds ratio confidence interval. Exclude paired data, repeated subjects, weights, regression and population risk estimation.

  skills/independent-2x2-categorical-comparison/SKILL.md on GitHub (opens in a new tab)

• junction-psi-and-delta-analysis

  Calculate descriptive PSI and between-group delta PSI from declared inclusion/exclusion counts and minimum coverage. Exclude alignment processing, event inference and significance testing.

  skills/junction-psi-and-delta-analysis/SKILL.md on GitHub (opens in a new tab)

• kaplan-meier-survival-analysis

  Estimate Kaplan-Meier survival from declared follow-up times and binary event indicators. Exclude log-rank tests, Cox models, competing risks and clinical recommendations.

  skills/kaplan-meier-survival-analysis/SKILL.md on GitHub (opens in a new tab)

• molecule-standardization-and-descriptors

  Clean SMILES/SDF records, normalize molecular structures and compute declared descriptors. Exclude similarity search, QSAR training and biological activity or mechanism claims.

  skills/molecule-standardization-and-descriptors/SKILL.md on GitHub (opens in a new tab)

No skill matches that filter.

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