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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.

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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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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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Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

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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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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

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Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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Calculates initial and escalating dose for pubertal induction hormone therapy based on patient weight or body surface area. Triggers include patient eligible for sex hormone treatment, ready to start hormones.

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This skill guides clinicians to inform and counsel individuals seeking gender-affirming medical treatment about fertility preservation options before initiating puberty suppression in adolescents or before starting hormonal therapy in adolescents and adults. It is triggered when a patient is eligible for pubertal suppression or sex hormone treatment and is about to begin such therapy.

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Recommends CSII over analog-based basal-bolus MDI for adults with T1DM who have not achieved their A1C goal, provided patient and caregivers are willing and able to use the device. Trigger phrases include 'Patient’s A1C is above target despite MDI' and 'Consider pump for uncontrolled T1DM'.

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Recommends discontinuation of GLP-1RA before conception rather than between start of pregnancy and end of first trimester for individuals with type 2 diabetes who are planning pregnancy. Trigger when clinician considers stopping GLP-1RA therapy in a patient with type 2 diabetes who is planning pregnancy or seeking preconception care.

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Suggests encouraging patients to use appropriately adjusted embedded bolus calculators in CSII and to provide education regarding their use and limitations. Triggers include: 'Patient starting pump, discuss bolus calculator', 'Review bolus calculator education at pump initiation'.

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This skill guides clinicians to assess bolus calculator settings when reviewing pump settings or verifying carb ratio and sensitivity factor during clinic visits. It evaluates insulin-to-carbohydrate ratio, insulin sensitivity factor, glucose targets, and active insulin time for embedded bolus calculators in CSII.

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Guidance for clinicians managing pregnant individuals with preexisting diabetes mellitus (PDM) who are evaluating daily carbohydrate intake; consider a carbohydrate-restricted diet (<175 g/day) or usual diet (>175 g/day) based on patient factors. Trigger when assessing nutrition in pregnancy for PDM, especially when discussing glycemic targets, weight gain, or fetal growth concerns.

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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 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 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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Recommends initiating intravenous bisphosphonate or denosumab for adults with hypercalcemia of malignancy compared with no treatment. Use when a clinician asks about first‑line pharmacologic therapy for HCM or when deciding to start antiresorptive agents.

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Recommends checking and managing vitamin D according to Endocrine Society guidelines to avoid hypocalcemia in patients receiving bisphosphonates or denosumab for hypercalcemia of malignancy. Use when a clinician notes risk factors for hypocalcemia (e.g., low 25‑OH vitamin D, renal insufficiency) and asks about baseline labs before antiresorptive start.

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Recommends mineralocorticoid receptor antagonists for all primary aldosteronism patients to prevent target organ damage, irrespective of blood pressure control or serum potassium levels. Triggered when a clinician encounters a PA patient with well‑controlled BP and normal K and wonders, 'Do I still need to treat with MRA?' or considers stopping therapy.

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