「eas」の検索結果

Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Calls HLA class I and class II alleles at 2/4/6/8-field resolution from WGS/WES/RNA-seq/long-read data using OptiType, HLA-LA, T1K, Polysolver, HLA-HD, arcasHLA, StarPhase, or HIBAG imputation. Use when typing for HSCT, solid-organ transplant, neoantigen prediction, PGx screening (B*57:01, B*15:02, etc.), or disease-association studies, with reconciliation across tools and IPD-IMGT/HLA version mismatch handling.

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Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.

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Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-suppression ladder (raw NGS ~1e-3 -> single-strand UMI ~1e-4/1e-5 -> duplex <1e-7), the CLSI EP17 LoB/LoD/LoD95/LoQ framework, the per-locus-vs-panel-integrated LoD distinction that lets bespoke MRD reach ppm, contrived/SEQC2 reference standards, and honest LoD reporting conditioned on input mass + consensus depth + replicate detection rate. Use when stating or trusting a sensitivity claim, designing a dilution-series validation, deciding how many genome equivalents are needed at a target VAF, choosing a single-locus vs panel-integrated LoD, or auditing a "detects 0.1% VAF" claim.

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Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.

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Infers genetic super-population ancestry from a 23andMe/AncestryDNA file and computes ancestry-stratified odds ratios with an exploratory Ancestry Elevation Score (AES) showing where ancestry-specific GWAS effect sizes diverge from European reference estimates.

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Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g. "get my model's eval score up", "improve this agent/harness", "tune this pipeline", "beat the baseline on this benchmark", "run a search over approaches and keep the best", "do an MLE-bench / Kaggle-style optimization", or any long-horizon "make this artifact better and don't just memorize the dev set" task. Trigger it even when the user doesn't say "Arbor" or "hypothesis tree" but describes repeated experiment-and-evaluate loops, branching exploration of competing ideas, or worries about a dev/test gap. Runs Claude itself as the coordinator with subagent executors in isolated git worktrees; for the standalone `arbor` CLI tool see references/arbor-upstream.md.

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This skill determines whether an adolescent or adult patient meets DSM-5 criteria for gender dysphoria (gender incongruence) by evaluating the presence of at least two of six specified criteria over a minimum 6-month duration, accompanied by clinically significant distress or impairment. It is triggered when a clinician queries whether the patient's reported symptoms align with gender dysphoria, such as persistent incongruence between experienced/expressed gender and designated gender.

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Determines whether bone mineral density (BMD) measurement is indicated when patients have osteoporosis risk factors or have discontinued sex hormone therapy following gonadectomy. Clinical triggers include documented osteoporosis risk factors (e.g., low body weight, glucocorticoid use, prior fracture) or cessation of sex hormone therapy after surgical gonadectomy.

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Suggests real-time CGM over no CGM for outpatients with type 2 diabetes who use insulin and/or sulfonylureas and are at high risk for hypoglycemia to detect and prevent low glucose events. Consider when initiating CGM in T2D patients on insulin/SU with a history of severe hypoglycemia or impaired awareness of hypoglycemia (IAH).

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Decide whether commonly-excluded patients (eating disorders, elderly ≥75, upper GI disease) can actually receive a GLP-1 receptor agonist. Use when a clinician asks "can I give semaglutide to a patient with binge eating disorder / anorexia / bulimia", "is liraglutide safe in an 80-year-old", "GLP-1 with GERD or chronic gastritis", "GLP-1 in sarcopenic elderly", or anytime a patient is being ruled out for GLP-1 therapy based on a perceived contraindication. Grounded in Gorgojo-Martínez 2023 §6 (Myths or Reality).

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This skill guides clinicians to reassess glucose monitoring frequency when discontinuing continuous subcutaneous insulin infusion (CSII) or transitioning to multiple daily injections (MDI). It is triggered by phrases such as 'Plan for glucose monitoring after pump stop' or 'Determine SMBG/CGM frequency post-pump' to ensure individualized glycemic goals are met.

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This skill reassesses the insulin plan when discontinuing continuous subcutaneous insulin infusion (CSII) and transitioning to multiple daily injections (MDI). It is triggered by phrases such as 'Review planned basal-bolus regimen after pump' and 'Confirm MDI dose calculations and schedule'.

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Recommends early delivery based on individualized risk assessment rather than expectant management for pregnant patients with preexisting diabetes mellitus (PDM). Consider when evaluating delivery timing in the presence of diabetes‑related complications, suboptimal glycemia, abnormal fetal growth, or maternal comorbidities that may increase perinatal risk beyond 38 weeks gestation.

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Suggests continuous subcutaneous insulin infusion (CSII) for adults with type 1 diabetes mellitus who desire increased insulin delivery flexibility or improved treatment satisfaction and are capable of using the device. Clinical triggers include statements such as 'Patient wants more lifestyle flexibility with insulin' or 'Consider pump for improved satisfaction in T1DM'.

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This skill suggests medical therapy to block aberrant hormone receptors for bilateral macronodular adrenal hyperplasia (BMAH) when surgery is not preferred or feasible. Consider this approach in patients with confirmed BMAH and evidence of aberrant hormone receptor expression (e.g., GIP, LH/hCG, serotonin) driving cortisol excess.

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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 suggests targeted therapies (somatostatin analogs or tyrosine kinase inhibitors) to treat ectopic ACTH syndrome when ectopic ACTH secretion is confirmed or strongly suspected. Use when triggers include occult or metastatic ectopic ACTH secretion, very severe ACTH‑dependent disease uncontrolled by medical therapy, or when surgery is not possible or noncurative.

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Recommends initial surgical resection of the primary lesion(s) causing Cushing's syndrome when surgery is feasible and likely to significantly reduce glucocorticoid excess. Trigger phrases include overt Cushing's syndrome, ACTH-dependent CS, ectopic ACTH secretion, adrenal adenoma, bilateral macronodular adrenal hyperplasia, and persistent hypercortisolism.

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