169 件 ・ 関連度順
概要と使いどころ
Systematically maps mechanism evidence for a disease from molecules to pathways, cell types, tissues, biological consequences, and clinical phenotypes. Always use this skill when a user needs a layered mechanism evidence chain rather than a flat summary or immediate gap analysis. Formal literature citations must be real and verifiable.
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Finds translational opportunities that connect basic-research discoveries to clinically meaningful use cases such as diagnosis, stratification, prognosis, treatment response prediction, monitoring, or therapeutic development. Use this skill when a user wants to turn a mechanism finding, pathway signal, cellular phenotype, experimental observation, or omics discovery into a stronger translational research direction. Always separate mechanistic relevance from translational usability, and never present a basic finding as clinically actionable unless the evidence supports that level.
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Organizes the evidence and competitive landscape around a drug, target, or pathway by separating disease relevance, tractability, preclinical evidence, clinical evidence, modality fit, and crowding. Always map what is biologically supported, what is druggable, what has actually advanced, and what remains strategically open. Never confuse target relevance with druggability, preclinical activity with clinical promise, or narrative excitement with validated development maturity. Never fabricate references, trial status, approval status, company activity, or asset metadata.
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Designs donor/repair templates for precise CRISPR knock-ins -- choosing the format (ssODN, long-ssDNA/Easi-CRISPR, dsDNA/plasmid, AAV6), sizing homology arms, placing the cut within ~10 bp of the edit, and adding a mandatory codon-checked blocking (PAM/seed) mutation so the edited allele is not re-cut. Frames the HDR-vs-NHEJ-vs-MMEJ pathway competition, the MMEJ (PITCh) and homology-independent (HITI/HMEJ) alternatives for post-mitotic cells, ssODN strand/asymmetry choice, phosphorothioate end-protection, and ranked HDR enhancers. Use when designing a donor for a point mutation, epitope/fluorophore tag, allele replacement, or knock-in, or when HDR efficiency is low. Guide design and base/prime editing are separate skills.
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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.
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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.
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Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-format export.
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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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Expert guidance for FedRAMP certification and compliance under CR26 (FedRAMP Consolidated Rules for 2026). Use this skill whenever a user asks about FedRAMP authorization, ATO (Authority to Operate), cloud security for federal government, NIST SP 800-53 controls, CSP compliance, or any of the core FedRAMP document types: SSP, SAP, SAR, POA&M, CIS/CRM workbooks. Also trigger for questions about FedRAMP Certification Classes (A, B, C, D — new baseline labels: A = pilot/transitional, B = LI-SaaS/Low, C = Moderate, D = High, per NTC-0004), FedRAMP 20x (now the primary authorization pathway), OSCAL mandate (September 2026), 3PAO assessments, continuous monitoring (ConMon), gap assessments, system boundary definition, or architecture reviews for federal cloud. FedRAMP Ready retired July 28, 2026 (Legacy FedRAMP Ready). When in doubt, use this skill — it covers the full FedRAMP lifecycle from readiness through continuous monitoring.
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Query KEGG pathway and molecular interaction network database
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Generates code that deploys fine-tuned models from SageMaker Serverless Model Customization to SageMaker endpoints or Bedrock. Use when the user says "deploy my model", "create an endpoint", "make it available", or asks about deployment options. Identifies the correct deployment pathway (Nova vs OSS), generates deployment code, and handles endpoint configuration.
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FDA regulatory consultant for medical device companies, covering 510(k)/PMA/De Novo pathways, QSR (21 CFR 820), HIPAA, and device cybersecurity. Use for FDA submissions, predicate and substantial-equivalence analysis, and premarket strategy.
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Expert guidance for FedRAMP certification and compliance under CR26 (FedRAMP Consolidated Rules for 2026). Use this skill whenever a user asks about FedRAMP authorization, ATO (Authority to Operate), cloud security for federal government, NIST SP 800-53 controls, CSP compliance, or any of the core FedRAMP document types: SSP, SAP, SAR, POA&M, CIS/CRM workbooks. Also trigger for questions about FedRAMP Certification Classes (A, B, C, D — new baseline labels: A = pilot/transitional, B = LI-SaaS/Low, C = Moderate, D = High, per NTC-0004), FedRAMP 20x (now the primary authorization pathway), OSCAL mandate (September 2026), 3PAO assessments, continuous monitoring (ConMon), gap assessments, system boundary definition, or architecture reviews for federal cloud. FedRAMP Ready retires July 28, 2026. When in doubt, use this skill — it covers the full FedRAMP lifecycle from readiness through continuous monitoring.
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Routes between five assessment pathways — formative, rubric/criteria, authentic/performance, peer/self, and diagnostic — with validity and equity checks. Use when a teacher needs help choosing how to assess.
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Pathview is a stand-alone software package for pathway based data integration and visualization.
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InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell comm
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ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
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KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essenti
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Select and verify the current region-specific serving container URI for a SageMaker model deployment. Use after the deployment pathway is chosen and before endpoint code; never infer an image URI from memory.
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Designs customer interviews and turns the transcripts into decisions. Produces an interview guide plus a synthesis (forces of progress, jobs, pathways, opportunities) you can paste into a doc. Use for 'customer interviews', 'discovery calls', 'JTBD', 'switch interview', 'who should I talk to', 'how many interviews', 'synthesize these transcripts', or 'why do customers churn/buy'. Draws on 140 Lenny's Podcast guests incl. Teresa Torres, Bob Moesta and Judd Antin.
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Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
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Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
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Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
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Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.
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