hcls-agent-skills

In the author's own words, from each skill's SKILL.md — showing the first 30 of 42 files.

• aws-genai-ml-architect

  Reasoning skill for designing AWS GenAI and ML architectures for healthcare and life sciences workloads. Use when the user asks to choose between SageMaker and Bedrock, design a RAG system over medical literature, architect clinical NLP or medical imaging inference, plan genomics or drug discovery pipelines on AWS, address HIPAA/PHI compliance in ML systems, design MLOps for regulated clinical mo…

  skills/aws-genai-ml-architect/SKILL.md on GitHub (opens in a new tab)

• bioinformatics-on-healthomics

  Guides users through bioinformatics analysis on AWS HealthOmics. Covers analysis type selection (alignment, variant calling, QC, interpretation), workflow generation in Nextflow or WDL, container sourcing from public registries, infrastructure setup (S3, ECR, IAM), workflow registration, parameter preparation, execution, and monitoring. Use when a user wants to run any bioinformatics pipeline on…

  skills/bioinformatics-on-healthomics/SKILL.md on GitHub (opens in a new tab)

• biomarker-discovery

  Reason about biomarker discovery and validation in HCLS — classifying biomarker intent, choosing feature-selection and cross-validation strategies, avoiding leakage, and planning external replication. Use when the user asks to discover, develop, or validate a biomarker; select features from high-dimensional omics or clinical data; design a validation study; choose evaluation metrics; justify samp…

  skills/biomarker-discovery/SKILL.md on GitHub (opens in a new tab)

• cdisc-compliance

  Reason about CDISC SDTM and ADaM implementation for regulatory submissions. Use when the user asks about SDTM domain mapping, ADaM dataset design, controlled terminology versioning, define.xml completeness, FDA or PMDA submission requirements, query prioritization by clinical impact, SUPPQUAL usage, or CDISC compliance review. Triggers include "SDTM mapping", "ADaM dataset", "CDISC compliance", "…

  skills/cdisc-compliance/SKILL.md on GitHub (opens in a new tab)

• cell-type-annotation

  Generate code to assign cell type labels to single-cell RNA-seq clusters using CellTypist, SingleR, marker-based annotation, or reference label transfer (scANVI/ingest). Triggers on requests to "annotate cell types", "label clusters", "run CellTypist", "SingleR annotation", "marker gene dotplot", "transfer labels from reference atlas", "cell identity", "automated annotation", "reference mapping",…

  skills/cell-type-annotation/SKILL.md on GitHub (opens in a new tab)

• cheminformatics

  Cheminformatics pipeline for small-molecule property calculation, filtering, and similarity analysis using RDKit. Use when the user asks to compute molecular descriptors, filter compounds by Lipinski or Veber rules, detect PAINS, calculate fingerprint similarity, run matched molecular pair analysis, generate ADMET descriptors, or process SMILES. Triggers include "RDKit", "molecular descriptors",…

  skills/cheminformatics/SKILL.md on GitHub (opens in a new tab)

• claims-analytics

  Pipeline skill for healthcare claims data parsing, analysis, and fraud detection. Use when the user asks to parse X12 837 or 835 claim files, manipulate ICD-10 CPT or HCPCS codes, detect billing pattern anomalies, profile providers against specialty peers, identify outlier billing behavior, validate NCCI edits programmatically, detect duplicate claims, run Benford's law analysis on charges, build…

  skills/claims-analytics/SKILL.md on GitHub (opens in a new tab)

• claims-billing-rules

  Reasoning skill for healthcare claims billing rules and fraud detection logic. Use when the user asks about CMS billing rules, place of service codes, global surgery periods, modifier usage (25 59 76 77), NCCI edit logic, column 1 column 2 code pairs, mutually exclusive procedures, modifier indicators, fraud waste and abuse patterns, E&M upcoding, unbundling, phantom billing, impossible day detec…

  skills/claims-billing-rules/SKILL.md on GitHub (opens in a new tab)

• clinical-data-standards

  Reason about clinical data terminology standards — MedDRA hierarchy (LLT→PT→HLT→HLGT→SOC), ICD-10 code structure and grouping, SNOMED CT concept model, LOINC panel relationships, and mapping decisions between systems. Use when the user asks to code adverse events, map diagnoses to ICD-10, choose a coding granularity level, group AEs by SOC or PT, interpret SNOMED CT relationships, select LOINC co…

  skills/clinical-data-standards/SKILL.md on GitHub (opens in a new tab)

• coordination-of-benefits

  Reasoning skill for Coordination of Benefits (COB) determination in healthcare claims. Use when a claim involves multiple insurers and the user needs to know which plan pays first, how to sequence billing, or why a COB-related denial or underpayment occurred. Covers Medicare Secondary Payer (MSP) rules and NAIC commercial COB order-of-benefits logic. Triggers include "coordination of benefits", "…

  skills/coordination-of-benefits/SKILL.md on GitHub (opens in a new tab)

• dicom-processing

  DICOM and NIfTI medical image processing pipeline. Triggers on DICOM, NIfTI, dcm2niix, de-identification, pydicom, DICOM header, conversion, anonymization, BIDS, DICOM tags, medical image format conversion, "DICOM to NIfTI", "burned-in PHI", "SeriesInstanceUID", "nibabel", "DICOM anonymization".

  skills/dicom-processing/SKILL.md on GitHub (opens in a new tab)

• digital-pathology

  Generate correct code for whole-slide image (WSI) analysis using TIAToolbox and foundation models (H-optimus-0, UNI, Prov-GigaPath). Triggers on requests involving whole-slide images, WSI, digital pathology, histopathology, SVS/NDPI/pyramidal TIFF, tissue segmentation, patch extraction, stain normalization, H-optimus-0, TIAToolbox, CAMELYON16/17, SlideGraph, MIL aggregation, HoVer-Net, PanNuke, o…

  skills/digital-pathology/SKILL.md on GitHub (opens in a new tab)

• drug-repurposing

  Reason about drug repurposing strategies in HCLS — choosing between target-based and phenotype-based approaches, evaluating mechanism-of-action overlap, querying drug-gene interaction databases, assessing clinical translatability, and ranking candidates by evidence strength. Use when the user asks to repurpose a drug, find approved drugs for a new indication, evaluate a repurposing candidate, que…

  skills/drug-repurposing/SKILL.md on GitHub (opens in a new tab)

• edc-data-validation

  Generate code for EDC export validation, clinical data range checks, cross-form consistency checks, SDTM structure validation, controlled terminology verification, and define.xml generation. Use when the user asks to validate clinical trial data exports, check vital sign or lab value ranges, verify AE date consistency, validate SDTM datasets against CDISC rules, generate define.xml, or build an a…

  skills/edc-data-validation/SKILL.md on GitHub (opens in a new tab)

• ehr-data-parsing

  Parse and extract clinical data from HL7v2 messages and FHIR R4 resources using Python. Use when the user mentions HL7v2, HL7, FHIR, PID segment, OBX segment, MSH segment, Patient resource, Observation resource, Condition resource, MedicationRequest, EHR data extraction, clinical message parsing, FHIR bundle, HL7 to FHIR conversion, ADT message, ORU message, lab result extraction, or clinical dat…

  skills/ehr-data-parsing/SKILL.md on GitHub (opens in a new tab)

• genomic-variant-interpretation

  Reason about germline and somatic variant classification using ACMG/AMP 2015 and AMP/ASCO/CAP frameworks. Use when the user asks to classify a variant, interpret a VCF annotation, resolve a VUS, apply ACMG criteria, weigh ClinVar evidence, evaluate gnomAD allele frequencies, interpret REVEL/CADD/SpliceAI scores, decide whether PVS1 applies, or assess gene-disease validity before reporting. Trigge…

  skills/genomic-variant-interpretation/SKILL.md on GitHub (opens in a new tab)

• hedis-measure-specification

  Reasoning skill for HEDIS measure specification, enrollment logic, exclusion evaluation, NCQA audit requirements, and care gap prioritization. Use when the user asks about HEDIS measure definitions, denominator/numerator/exclusion logic, continuous enrollment rules, Star Rating impact, or care gap closure strategies.

  skills/hedis-measure-specification/SKILL.md on GitHub (opens in a new tab)

• imaging-study-design

  Reasoning skill for medical imaging study design and biomarker selection. Use when the user asks to plan an imaging study, choose a preprocessing strategy, select an imaging biomarker, design a radiomics pipeline, handle DICOM de-identification, plan longitudinal imaging analysis, or pick a registration target. Triggers include "imaging study", "preprocessing strategy", "DICOM de-identification",…

  skills/imaging-study-design/SKILL.md on GitHub (opens in a new tab)

• medical-device-software-compliance

  Reason about SaMD (Software as a Medical Device) regulatory compliance for FDA, EU MDR, and global submissions. Use when the user asks about IEC 62304 safety classification, ISO 14971 risk management, 21 CFR 820/QMSR quality system requirements, Design History File structure, 510(k)/De Novo/PMA pathway selection, SOUP/OTS assessment, verification and validation planning, cybersecurity for medical…

  skills/medical-device-software-compliance/SKILL.md on GitHub (opens in a new tab)

• ml-researcher

  Reason about ML experiment design for healthcare and life sciences data. Use when the user asks to design an ML study, choose a model for clinical/biomedical data, set up cross-validation, pick evaluation metrics, audit fairness, plan a regulatory submission, or critique an ML pipeline on EHR, medical imaging, genomics, molecules, or clinical text. Triggers include "design an ML experiment", "whi…

  skills/ml-researcher/SKILL.md on GitHub (opens in a new tab)

• molecular-docking

  Molecular docking pipeline using AutoDock Vina for structure-based drug discovery. Triggers on docking, AutoDock Vina, receptor preparation, ligand preparation, PDBQT, grid box, virtual screening, binding affinity, pose prediction, structure-based virtual screening, "redocking RMSD", "Vina score", "docking pose", "prepare receptor", "ligand library screening".

  skills/molecular-docking/SKILL.md on GitHub (opens in a new tab)

• multi-omics-integration

  Reasoning skill for multi-omics data integration strategy selection. Use when the user asks to integrate transcriptomics with proteomics, combine multi-omic layers, choose between early intermediate or late integration, apply batch correction across omics, handle partial sample overlap, run MOFA+ or iCluster, interpret multi-omic factors, select enrichment methods for multi-omic signatures, or de…

  skills/multi-omics-integration/SKILL.md on GitHub (opens in a new tab)

• multi-omics-pipeline

  Pipeline skill for multi-omics data processing and integration. Use when the user asks to map gene IDs between HGNC Ensembl and UniProt, convert between omic data formats, run batch correction with ComBat or ComBat-seq, perform GSEA or over-representation analysis on multi-omic results, run consensus clustering on integrated data, execute MOFA2 in R or mofapy2 in Python, build a multi-omics ETL p…

  skills/multi-omics-pipeline/SKILL.md on GitHub (opens in a new tab)

• ngs-quality-control

  NGS quality control pipeline for short-read sequencing data. Triggers on FastQC, QC, quality control, adapter trimming, coverage, mosdepth, Picard metrics, fastp, MultiQC, sequencing QC, BAM QC, WGS/WES coverage analysis.

  skills/ngs-quality-control/SKILL.md on GitHub (opens in a new tab)

• pa-clinical-policy

  Reasoning skill for prior authorization clinical policy evaluation. Use when the user asks about payer clinical criteria, step therapy requirements, medical necessity definitions, CMS LCD/NCD coverage rules, appeals documentation strategy, formulary tier implications, or FHIR Da Vinci PAS implementation guidance. Triggers include "prior auth policy", "step therapy", "medical necessity", "coverage…

  skills/pa-clinical-policy/SKILL.md on GitHub (opens in a new tab)

• pa-decision-automation

  Pipeline skill for automating prior authorization decision workflows. Use when the user asks to parse PA request data (X12 278 or FHIR PAS bundles), extract clinical features for adjudication, build rules-based PA decision engines, train ML classifiers on historical PA decisions, analyze denial patterns, or generate SHAP explanations for PA outcomes. Triggers include "parse 278", "FHIR PAS bundle…

  skills/pa-decision-automation/SKILL.md on GitHub (opens in a new tab)

• pharmacoepidemiology

  Reason about pharmacoepidemiologic study design for causal inference from real-world data — choosing active comparator new-user designs, emulating target trials, avoiding immortal time bias, handling time-varying confounding with marginal structural models, and selecting propensity score methods. Use when the user asks to design a drug safety or effectiveness study, choose between propensity scor…

  skills/pharmacoepidemiology/SKILL.md on GitHub (opens in a new tab)

• protein-structure-analysis

  Pipeline skill for protein structure analysis covering PDB/mmCIF parsing, RMSD superposition, Ramachandran/dihedral analysis, binding pocket detection, contact maps, B-factor flexibility, DSSP secondary structure, and format conversion. Triggers on PDB, protein structure, RMSD, Ramachandran, binding pocket, Biopython, PyMOL, pocket detection, fpocket, DSSP, PDBQT, structural alignment, superposit…

  skills/protein-structure-analysis/SKILL.md on GitHub (opens in a new tab)

• provider-denial-workup

  Reasoning skill for healthcare revenue cycle denial management. Use when the user needs to appeal a claim denial, draft a payer-ready denial appeal letter, analyze a denial reason code, or determine whether a denied claim should be overturned, pended, or accepted. Triggers include "appeal a claim denial", "draft denial appeal", "write appeal letter", "CO-50 denial", "medical necessity denial", "C…

  skills/provider-denial-workup/SKILL.md on GitHub (opens in a new tab)

• quality-measures

  Pipeline skill for computing HEDIS quality measures from claims and clinical data. Use when the user asks to calculate HEDIS measure rates, check continuous enrollment, build denominator/numerator logic, detect care gaps, compute utilization rates, identify high-cost claimants, or score risk stratification indices. Triggers include "calculate HEDIS", "measure rate", "continuous enrollment check",…

  skills/quality-measures/SKILL.md on GitHub (opens in a new tab)

No skill matches that filter.

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