257 件 ・ 関連度順
概要と使いどころ
Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.
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Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.
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Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, navigating SuperSeries vs SubSeries, choosing between series-matrix (submitter-normalized) and raw supplementary files, downloading via GEOparse (Python) or GEOquery (R/Bioconductor), linking GEO to SRA for raw reads, or distinguishing GSE/GSM/GPL/GDS record types. Encodes the SuperSeries trap, the series-matrix normalization-trust caveat, GEOmetadb deprecation, ArrayExpress migration to BioStudies, and processed-vs-raw decision matrix.
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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.
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Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.
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Think and work like an expert Medicinal Chemist. Use when a task calls for Medicinal Chemist judgment. Reasons from structure-activity relationships, lipophilicity and unbound-fraction physicochemistry, synthetic accessibility, and target-product-profile multiparameter optimization through LLE/Fsp3/QED scoring, FEP+/Glide docking validated against co-crystal and SPR data, ELN-tracked LC-MS/NMR synthesis, and DMPK panels (microsomal CL, Caco-2 efflux, hERG, CYP) while treating PAINS and aggregation assay artifacts, biochemical-versus-cellular potency gaps, reactive-metabolite soft spots, and freedom-to-operate cliffs as first-class failure modes.
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Think and work like an expert Molecular Neuroscientist. Use when a task calls for Molecular Neuroscientist judgment. Reasons from NPQ transmission, AMPAR/NMDAR trafficking, monoamine receptor/transporter systems, optogenetics (ChR2/Chrimson/ACR) with retinal-artifact controls, AAV/rabies circuit tracing, and region RNA-seq with DESeq2/SynGO—integrating synaptic biochemistry, perturbation, and omics while treating mini-detection bias, TVA leak, and batch/composition confounds as first-class failure modes.
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Think and work like an expert Corrosion Engineer. Use when a task calls for Corrosion Engineer judgment. Reasons from electrochemical couples, Pourbaix/galvanic selection, and ISO 15156 sour-service limits through AMPP SP0169/SP0502 CP and ECDA, CO₂ models (NORSOK M-506, OLI), coupon/ER/LPR monitoring, and ASTM G5/G48/G61 qualification while treating IR-masked CIPS, salt-spray overclaim, MIC vs. biocide residual, and MR0175≠fit-for-service as first-class failure modes.
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Think and work like an expert Biomedical Engineer. Use when a task calls for Biomedical Engineer judgment. Reasons from ISO 14971 risk management, ISO 10993 biocompatibility matrices, ASTM F/ISO 14242 mechanical and wear testing, and FDA 510(k) substantial equivalence; treats stress shielding, UHMWPE osteolysis, F2129 corrosion artifacts, and predicate/material mismatches as first-class failure modes.
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Think and work like an expert Agricultural Entomologist. Use when a task calls for Agricultural Entomologist judgment. Reasons from pest population dynamics, economic injury levels and thresholds, and degree-day phenology through systematic scouting, IRAC mode-of-action rotation, RCBD efficacy trials, and conservation biocontrol while treating misidentification, secondary pest flares from enemy removal, resistance under repeated MoA, and trap-catch-without-field-verification as first-class failure modes.
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Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.
日本語の概要は準備中です。原文の説明を表示しています。
Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.
日本語の概要は準備中です。原文の説明を表示しています。
Proteina-Complexa flow-based protein backbone generation with fold-conditioned sampling guidance. Use this skill when: (1) Generating de novo protein backbones with hierarchical fold conditioning, (2) Exploring long-chain backbone generation beyond standard diffusion baselines, (3) Using NVIDIA Proteina-style flow matching workflows for controllable backbone design, (4) Comparing flow-based backbone generation against RFdiffusion or BoltzGen, (5) Prototyping fold-guided backbone campaigns before sequence design. This skill is based on the public NVIDIA Digital Bio Proteina project and uses "Proteina-Complexa" as the BioClaw-facing skill label. For sequence design after backbone generation, use proteinmpnn or solublempnn. For QC thresholds, use protein-design-qc.
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Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks about available skills, advanced workflows, or specialized analysis pipelines. Triggers on "skills hub", "more skills", "install skill", "community skills", "find a skill for".
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Applies the strategic thinking of Kiran Mazumdar-Shaw, founder of Biocon and pioneering Indian biopharmaceutical entrepreneur. Use this skill whenever you are advising on biotech startups, R&D innovation, global scaling, purpose-driven business, or navigating regulatory uncertainty. Trigger this skill when discussing affordable healthcare, balancing risk in long-gestation industries, breaking glass ceilings through credible success, or evaluating biotech sovereignty and AI. Reach for this skill even if the user doesn't name her, especially when they face career trade-offs, funding novel scientific ideas, or scaling manufacturing globally.
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Foundational concepts in nutrition science — macronutrients, micronutrients, energy balance, Atwater factors, reference intakes (DRI/RDA/AI/UL), food composition tables, and the methods of human nutrition research. Grounds the rest of the department in a shared vocabulary and in the measurement limits of the field, including controlled-trial history, observational-study limits, and the biochemical basis for calorie accounting. Use when a question asks what something "is" nutritionally, how energy and nutrients are measured, or what the reference numbers mean.
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Carbon chemistry, functional groups, IUPAC nomenclature, isomerism, reaction mechanisms (substitution, elimination, addition), polymers, and biochemistry basics. Covers hydrocarbon classes (alkanes, alkenes, alkynes, aromatics), common functional groups (alcohols, aldehydes, ketones, carboxylic acids, esters, amines, amides), stereochemistry, condensation and addition polymerization, and the four biomolecule classes (carbohydrates, lipids, proteins, nucleic acids). Use when analyzing organic structures, predicting reaction products, or connecting chemistry to biology.
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Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
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This skill recommends against initiating treatments aimed at normalizing cortisol or its action when only borderline biochemical abnormalities of the hypothalamic-pituitary-adrenal (HPA) axis are present without specific signs of Cushing's syndrome. Use when encountering borderline urinary free cortisol, late-night salivary cortisol, or dexamethasone suppression test results without classic Cushingoid features; triggers include borderline UFC (1-2× ULN), equivocal late-night salivary cortisol, or nondiagnostic low-dose DST.
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This skill recommends unilateral resection by an experienced adrenal surgeon for all cases of benign unilateral disease causing Cushing's syndrome. Trigger when a CS patient has a unilateral adrenal lesion confirmed benign via imaging and biochemical assessment.
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This skill directs lifelong treatment of cardiovascular risk factors, osteoporosis, and psychiatric symptoms in all patients with Cushing's syndrome until biochemical resolution of hypercortisolism. Use when managing any CS patient for long‑term comorbidity control; triggers include persistent hypertension, dyslipidemia, low bone density, depression, anxiety, or cognitive changes in the setting of known or suspected CS.
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This skill recommends lifelong biochemical testing for recurrence in all patients with Cushing's syndrome after adrenalectomy, except those with resected adrenal adenoma showing CT density <10 Hounsfield units. Use when determining long‑term follow‑up strategy for a post‑adrenalectomy CS patient; triggers include “post‑adrenalectomy Cushing’s syndrome”, “CT density <10 HU”, and “adrenal adenoma resection”.
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This skill recommends using biochemical tests to screen for hypercortisolism to detect recurrence in patients with ACTH-dependent Cushing's syndrome after surgical remission. It is triggered during postoperative follow-up when the HPA axis has recovered, annually, or sooner if clinical signs of hypercortisolism (e.g., weight gain, hypertension, glucose intolerance) or abnormal late-night salivary cortisol/UFC appear.
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This skill recommends obtaining a postoperative pituitary MRI within 1–3 months after successful transsphenoidal surgery (TSS) to establish a new baseline for future recurrence assessment. Use when a Cushing’s syndrome patient has achieved biochemical remission post‑TSS and is entering routine follow‑up.
日本語の概要は準備中です。原文の説明を表示しています。