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Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution, mRNA:gene ratio, coding density). Covers the assembly-BUSCO-vs-proteome-BUSCO diagnostic, what BUSCO-Duplicated really means, why gene count is a vanity metric, and the QC of transferred annotations. Use when judging whether an annotation is good enough to publish or submit, diagnosing a suspect annotation, or comparing annotation completeness across pipelines.

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Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.

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Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.

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Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.

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Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.

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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

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Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Expert guide for Backend.AI distributed computing platform. Automatically activates when users ask about: - Backend.AI architecture, components (Manager, Agent, Storage Proxy, Webserver, App Proxy) - Features (session scheduling, Sokovan orchestrator, multi-tenancy, resource allocation) - APIs (REST, GraphQL), authentication, RBAC authorization - Container runtime (kernels, jail sandbox, hook library, virtual folders) - Accelerator support (CUDA, ROCm, TPU, NPU, Graphcore IPU) - Client SDKs (Python, Java, JavaScript, PHP) - Setup, requirements (Python 3.13+, Docker, PostgreSQL, Redis, etcd) - How WebUI connects to/interacts with Backend.AI backend - Plugin interfaces, development setup, infrastructure Use when user mentions "Backend.AI", "backend.ai", "Sokovan", component names, or asks about the backend platform this WebUI connects to. allowed-tools: WebFetch, Read

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Search scientific papers via the BGPT MCP server and retrieve structured experimental data — methods, results, conclusions, quality scores, and 25+ metadata fields per paper.

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This skill provides AWS cost optimization, monitoring, and operational best practices with integrated MCP servers for billing analysis, cost estimation, observability, and security assessment.

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Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what they actually do. Requires the screenpipe daemon (https://github.com/screenpipe/screenpipe) running locally on port 3030 — the skill has no other data source and will refuse to run if screenpipe is unreachable. All detection runs locally; only redacted cluster summaries reach the LLM.

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Recommends continuing insulin pump therapy in hospitals with pump expertise; otherwise transitioning to scheduled subcutaneous basal bolus insulin if anticipated length of stay exceeds 1–2 days before pump discontinuation. Consider this when anticipating a hospital stay >2 days, lacking pump expertise, or needing to conserve supplies.

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Determines whether a hypertensive patient should be screened for primary aldosteronism based on clinical features associated with higher PA prevalence. Triggered when a clinician asks 'Should I screen this hypertensive patient for PA?' or observes spontaneous hypokalemia, resistant hypertension, hypertension onset before age 40, adrenal tumor, young-onset stroke, or sleep apnea syndrome.

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Recommends denosumab for adults with refractory or recurrent hypercalcemia of malignancy who have persistent or relapsed hypercalcemia despite intravenous bisphosphonate therapy. Triggered when a clinician observes recurrent hypercalcemia after bisphosphonate treatment or considers next‑line agents for HCM.

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Recommends immediate IV hydrocortisone stress dosing for patients with suspected adrenal crisis presenting with severe adrenal insufficiency symptoms such as hypotension, hyponatremia, hyperkalemia, or acute abdominal pain. Use when clinician observes signs of adrenal crisis (e.g., syncope, delirium, marked abdominal tenderness) prior to diagnostic test results.

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Recommends performing biochemical testing for HPA axis at least 18-24 hours after last hydrocortisone dose or longer for synthetic glucocorticoids. Use when scheduling HPA axis testing in glucocorticoid-treated patient needing assessment of adrenal reserve.

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Accounts for estrogen-induced elevation of total serum cortisol via increased corticosteroid-binding globulin (CBG) when evaluating adrenal reserve or hydrocortisone replacement adequacy. Triggered when assessing glucocorticoid adequacy in patients receiving estrogen therapy (e.g., oral estrogen replacement) or interpreting cortisol levels in estrogen-exposed individuals.

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Drift check between the baseline implementation on disk and the claims in `docs/init/seed.md` + cross-references in CLAUDE.md, README.md, and the rendered docs site. Verifies hook/agent/skill/command names + counts, settings.json wiring, project.json key presence, .mcp.json servers, vendored license files, and helper script presence. Exit 0 PASS / 1 FAIL — suitable for CI. Read-only; safe to invoke any time.

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Analyze a codebase and recommend Claude Code automations (hooks, subagents, skills, plugins, MCP servers). Use when user asks for automation recommendations, wants to optimize their Claude Code setup, mentions improving Claude Code workflows, asks how to first set up Claude Code for a project, or wants to know what Claude Code features they should use.

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MCP client: connect servers, register tools (stdio/HTTP).

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Generate architecture diagrams with draw.io in headless/server environments (WSL2, VPS, Docker)

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