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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Detect Neanderthal and Denisovan introgression segments from modern human genomes

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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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Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus structured JSON for downstream chaining.

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This skill recommends re-evaluating the need for treatment of other pituitary hormone deficiencies in the postoperative period following surgical intervention for Cushing's syndrome. It is triggered when assessing a post-op CS patient for ongoing pituitary function, evaluating for hypopituitarism, or checking HPA axis recovery with morning cortisol/ACTH stimulation tests and pituitary MRI within 1–3 months.

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This skill suggests pituitary-directed medical treatments (e.g., cabergoline, pasireotide) for patients with Cushing's disease who are not surgical candidates or have persistent disease after transsphenoidal surgery. Use when a CD patient cannot undergo surgery or has residual disease post-TSS; triggers include "not a surgical candidate", "persistent disease after TSS", "ongoing hypercortisolism despite prior surgery".

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This skill recommends transsphenoidal selective adenomectomy (TSS) by an experienced pituitary surgeon as the optimal treatment for Cushing's disease in pediatric and adult patients. Use when a patient with ACTH-dependent Cushing syndrome is a surgical candidate; triggers include overt Cushing's syndrome, elevated UFC or late-night salivary cortisol, and pituitary MRI showing an adenoma.

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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 provides a shared decision-making framework for selecting second-line therapies in patients with ACTH-dependent Cushing's syndrome who have persistent hypercortisolism after transsphenoidal surgery or for whom surgery is not feasible. Clinical triggers include "failed TSS", "non-curative pituitary surgery", "persistent UFC elevation post-op", and "surgery contraindicated".

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This skill recommends using radiation therapy for corticotroph adenomas in Cushing's disease when imaging shows invasive features or mass‑effect concerns such as cavernous sinus invasion, suprasellar extension, or knobby protrusion. Consider RT when postoperative medical therapy has normalized cortisol but tumor progression or residual invasive disease is suspected.

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This skill recommends that a multidisciplinary team, including an experienced endocrinologist, incorporates patient values and preferences while providing education about treatment options for Cushing’s syndrome. Use when planning treatment for a CS patient requiring coordinated care; triggers include persistent hypercortisolism after transsphenoidal surgery, consideration of bilateral adrenalectomy, radiotherapy, or medical therapy, and need for shared decision‑making.

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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 localizing and resecting ectopic ACTH-secreting tumors with node dissection when ectopic ACTH secretion is suspected or confirmed. Clinical triggers include unexplained persistent hypercortisolism after pituitary surgery, elevated ACTH with negative pituitary MRI, or identification of occult ectopic ACTH syndrome (EAS) on biochemical testing.

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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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This skill suggests administering a glucocorticoid antagonist (e.g., mifepristone) in patients with Cushing's disease who have diabetes or glucose intolerance and are not surgical candidates or have persistent disease after transsphenoidal surgery. Consider when encountering persistent hypercortisolism after TSS, contraindications to surgery, or comorbid diabetes/glucose intolerance requiring medical control.

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This skill recommends educating patients and families about the clinical features of remission in Cushing's syndrome when a patient achieves biochemical remission after treatment. Use when a CS patient has postoperative normal cortisol levels, reports symptom improvement, and requires guidance on long-term expectations and monitoring for recurrence.

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This skill recommends discontinuing glucocorticoid when the response to HPA axis recovery tests (morning cortisol, ACTH stimulation, or insulin-induced hypoglycemia) is normal, indicating adequate adrenal function recovery. Use in postoperative Cushing’s syndrome patients with at least one intact adrenal gland when test results are available.

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This skill confirms that medical therapy has normalized cortisol before initiating radiation therapy or radiosurgery for Cushing's syndrome to maintain disease control while awaiting radiation effect. It is triggered when planning pituitary RT/radiosurgery for a patient with persistent or recurrent Cushing's disease after transsphenoidal surgery (TSS) or when medical therapy is being used as a bridge to radiation.

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This skill recommends urgent treatment (within 24–72 hours) of hypercortisolism when life‑threatening complications of Cushing's syndrome such as infection, pulmonary thromboembolism, cardiovascular events, or acute psychosis are present. Trigger phrases include sepsis, PE, chest pain with hemodynamic instability, new‑onset psychosis, or delirium in a patient with known or suspected Cushing's.

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This skill recommends bilateral adrenalectomy for occult or metastatic ectopic ACTH secretion or as a life-preserving emergency treatment in patients with very severe ACTH‑dependent Cushing’s syndrome who cannot be promptly controlled by medical therapy. It is triggered by life‑threatening complications of uncontrolled hypercortisolism such as infection, pulmonary thromboembolism, cardiovascular catastrophe, or acute psychosis.

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This skill recommends against initiating cortisol-lowering treatment when there is no established diagnosis of Cushing's syndrome. It is triggered when a clinician considers treating suspected CS based only on borderline biochemical abnormalities or nonspecific signs without confirmatory testing; examples include "suspected CS", "borderline UFC", "no confirmed diagnosis", "consider empiric ketoconazole".

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Determines successful catheterization in adrenal venous sampling by applying selectivity index cut‑offs with and without ACTH stimulation. Triggered during AVS when measuring cortisol levels and asking “Is the catheter properly positioned?” or when reviewing results for technical adequacy.

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Recommends initiating intravenous isotonic saline hydration as initial management for hypercalcemia of malignancy (HCM) while awaiting antiresorptive therapy, with fluid rate adjusted according to cardiac function. Triggered when a clinician encounters a patient with HCM (e.g., serum calcium >12 mg/dL, symptoms of hypercalcemia) and seeks immediate measures before specific drugs are available.

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Identifies safe antihypertensive options for hypertensive disorders in pregnancy applicable to PA patients, with gestational age restrictions. Triggers include when managing hypertension in a pregnant or pregnancy-planning PA patient and asking 'What BP meds are safe?' or reviewing medications.

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