Results for “clinical”

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

Extracts selected metadata from a DICOM file and flags standard-tag PHI presence. Not for anonymization or clinical use.

Engages users in structured philosophical and psychological conversations, blending clinical frameworks with wisdom traditions for self-exploration and emotional support.

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels.

Maps FHIR R4 clinical resources (Patient, Observation, Condition, CarePlan, CodeableConcept) to Salesforce Health Cloud objects, including prerequisite configuration and cardinality handling.

NIH grant research skill for clinical researchers. Grill-me intake (research idea + career stage + preliminary data + environment + submission posture + known institute targets) locks down the funding strategy before any search runs. Runs a 5-face...

Queries the ClinPGx REST API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels, generating markdown reports with CSV tables.

Query NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assessing whether a variant is pathogenic, likely pathogenic, VUS, likely benign, or benign, resolving conflicting interpretations, or annotating a VCF with ClinVar clinical significance. For population allele frequencies by ancestry use alterlab-gnomad; for somatic cancer mutation frequencies use alterlab-cosmic. Part of the AlterLab Academic Skills suite.

Use when deciding which jama-* sub-skill to invoke next, or when sequencing a clinical manuscript from scope check through revision for JAMA (Journal of the American Medical Association). Routes — does not replace — the specialized skills.

Use when deciding which nejm-* sub-skill to invoke next, or when sequencing a clinical manuscript from significance test through response to reviewers for The New England Journal of Medicine. Routes — it does not replace — the specialized skills.

Use before sensitive, clinical, identifying, or raw interview data is placed in front of an AI tool, when transcripts or student materials need de-identification, or when a data-minimization gate must run before any analysis or drafting.

Use to structure and tighten an NEJM Original Article into terse IMRAD — short main text (~2700 words), limited references, claim-first results, and a sober discussion with explicit limitations and calibrated clinical implications. Enforces NEJM's plain, concise house style.

Guides comorbidity-stratified selection of initial and further glucose-lowering medicines for adults with type 2 diabetes using the NICE NG28 (2026) framework, covering six clinical profiles: no relevant comorbidity, heart failure, atherosclerotic cardiovascular disease, early onset, obesity, chronic kidney disease, and frailty.

Use to confirm clinical ethics and research-integrity requirements for an NEJM submission — IRB/ethics-committee approval and informed consent per the Declaration of Helsinki, ICMJE conflict-of-interest disclosures and authorship criteria, the role-of-the-funding-source statement, and the ICMJE data-sharing statement.

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.

Use when scoping a project and before any writing, to stress-test whether a study clears The Lancet's bar — clinically or public-health important, globally relevant, and likely to change practice or policy, often with an equity lens. Decides The Lancet vs a Lancet family title vs another general medical journal.

Recommends confirmatory testing with corticotropin stimulation test in patients presenting with clinical symptoms or signs suggesting PAI (e.g., fatigue, hypotension, hyponatremia, hyperpigmentation) when the patient's condition permits safe testing. Use when a clinician identifies suggestive features and circumstances allow outpatient stimulation testing without imminent need for emergency glucocorticoids.

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

Calculates the lowest effective glucocorticoid dose (dexamethasone or prednisone) to normalize blood pressure and serum potassium in glucocorticoid-remediable aldosteronism (GRA/FH-I) by titrating to biochemical and clinical targets. Indicated when initiating medical treatment for confirmed GRA, triggered by findings such as early-onset hypertension, family history of stroke before age 40, spontaneous hypokalemia, or suppressed plasma renin activity with elevated aldosterone.

Drafts attorney-supervised, state-compliant U.S. Advance Health Care Directives that appoint health care agents, resolve the HIPAA access gap, and record clinically usable treatment preferences. Enforces state-law verification for execution formalities, statutory forms, and special limitations. Addresses adversarial risks from family disputes and institutional challenges. Use when drafting advance directives, health care proxies, living wills, health care powers of attorney, HIPAA medical authorizations, or end-of-life planning documents.

Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing, checking PGx drug-safety associations (e.g. HLA-B*57:01 and abacavir), or supporting precision medicine and clinical pharmacogenomics decisions. For star-allele definitions/frequencies see PharmVar; for germline/somatic variant pathogenicity see alterlab-clinvar. Part of the AlterLab Academic Skills suite.

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional tracks from a DNA sequence, scoring a non-coding/regulatory variant's effect on expression or chromatin, or doing in-silico mutagenesis of a locus. To LOOK UP a variant's population frequency prefer alterlab-gnomad; for its clinical significance prefer alterlab-clinvar; for protein-structure effects prefer alterlab-alphafold; for single-cell foundation models prefer alterlab-scgpt. Part of the AlterLab Academic Skills suite.

NIH grant research skill for clinical researchers. Grill-me intake (research idea + career stage + preliminary data + environment + submission posture + known institute targets) locks down the funding strategy before any search runs. Runs a 5-facet Consensus positioning analysis (with draft Significance/Innovation language), maps the research to the right NIH institutes and study sections via RePORTER, finds NOSIs and funded overlap, and produces an editable Word document (.docx) with budget/scope-aware mechanism recommendations, submission timelines, and a mandatory program officer recommendation. Use when the user asks about research funding or makes any grant-related request (e.g., 'grants for [topic]', 'find grants for my research idea', 'what grants match my research', 'help me find NIH funding', 'grant opportunities for my research'). NIH-only scope — non-NIH funders (PCORI, DOD CDMRP, VA, foundations) are out of scope and flagged at intake.