Processing
Data transformation and parsing
gnomad-database
by jaechang-hits
"Query gnomAD v4 population variant frequencies via GraphQL API. Retrieve allele counts and frequencies stratified by ancestry group (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID), gene-level constraint metrics (pLI, LOEUF, missense z-score), and read depth coverage. Identify variants with low population frequency or under evolutionary constraint. For clinical pathogenicity classifications use clinvar-database; for GWAS associations use gwas-database."
pyimagej-fiji-bridge
by jaechang-hits
"Python bridge to ImageJ2/Fiji enabling macro execution, plugin calls (Bio-Formats, TrackMate, Analyze Particles), bidirectional NumPy↔ImagePlus/ImgLib2 data exchange, and ImageJ Ops from Python. Use for automating Fiji-specific workflows headlessly from Python scripts. Use scikit-image instead for pure Python pipelines that do not require Fiji plugins; use napari for interactive visualization."
gget-genomic-databases
by jaechang-hits
"Unified CLI/Python interface to 20+ genomic databases. Use for quick gene lookups (Ensembl search/info/seq), BLAST/BLAT sequence alignment, AlphaFold structure prediction, enrichment analysis (Enrichr), disease/drug associations (OpenTargets), single-cell data (CELLxGENE), cancer genomics (cBioPortal/COSMIC), and expression correlation (ARCHS4). Covers genomics, proteomics, and disease domains. For batch processing or advanced BLAST use biopython; for multi-database Python SDK workflows use bioservices."
clinpgx-database
by jaechang-hits
"Query PharmGKB (Clinical Pharmacogenomics) database via REST API for drug-gene interactions, clinical annotations, dosing guidelines (CPIC, DPWG), variant-drug associations, and pharmacogenomic pathways. Search by gene, drug, rsID, or pathway. No authentication required. For somatic cancer pharmacogenomics use cosmic-database or opentargets-database; for drug structures use chembl-database-bioactivity."
nnunet-segmentation
by jaechang-hits
"Train and deploy automated medical image segmentation models using nnU-Net's self-configuring framework that auto-selects optimal architecture, preprocessing, and training for any modality. Supports CT, MRI, microscopy, and ultrasound with 2D, 3D full-res, 3D low-res, and cascade configurations. Pipeline: convert dataset → plan and preprocess → train (5-fold cross-validation) → find best configuration → predict → ensemble. Use when classical segmentation fails and annotated training data is available."
deseq2-differential-expression
by jaechang-hits
"Differential expression analysis for bulk RNA-seq using R/Bioconductor DESeq2. Negative binomial GLM with empirical Bayes shrinkage, Wald and LRT tests, multi-factor designs, interaction terms, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap visualization. The R gold standard for DE analysis with native Bioconductor integration. Use pydeseq2-differential-expression for Python-based pipelines; use edgeR for TMM normalization."
cosmic-database
by jaechang-hits
"Query COSMIC (Catalogue Of Somatic Mutations In Cancer) for cancer somatic mutations, gene census data, mutational signatures, drug resistance variants, and cancer gene annotations. REST API v3.1 supports gene/sample/variant queries. Free registration required. For germline clinical variants use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity."
ena-database
by jaechang-hits
"European Nucleotide Archive (ENA) REST API access for genomic sequences, raw reads, assemblies, and annotations. Portal API search with query syntax, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM download URLs, taxonomy queries, cross-references. For multi-database Python queries prefer bioservices; for NCBI-specific queries use pubmed-database or Biopython Entrez."
creating-styled-wrappers
by tambo-ai
Creates styled wrapper components that compose headless/base compound components. Use when refactoring styled components to use base primitives, implementing opinionated design systems on top of headless components, or when the user mentions "use base components", "compose primitives", "styled wrapper", or "refactor to use base".
cellxgene-census
by jaechang-hits
"Query CELLxGENE Census (61M+ cells) programmatically. Search by cell type, tissue, disease, organism. Get expression matrices as AnnData, stream large queries out-of-core, train PyTorch models on single-cell data. For analyzing your own data use scanpy; for annotated data manipulation use anndata."
pydicom-medical-imaging
by jaechang-hits
"Pure Python DICOM library for medical imaging (CT, MRI, X-ray, ultrasound). Read/write DICOM files, extract pixel data as NumPy arrays, access/modify metadata tags, apply windowing (VOI LUT), anonymize PHI, build DICOM from scratch, process series into 3D volumes. For whole-slide pathology images use histolab; for NIfTI neuroimaging use nibabel."
simpleitk-image-registration
by jaechang-hits
"Register, segment, filter, and resample 3D medical images (MRI, CT, microscopy) using SimpleITK's Python API with support for DICOM, NIfTI, and multi-modal image analysis. Provides rigid/affine/deformable registration, threshold and region-growing segmentation, Gaussian and morphological filtering, label statistics, and format conversion. Use when aligning volumetric images across timepoints or modalities, automating segmentation of fluorescence microscopy, or converting DICOM series to NIfTI for analysis pipelines."
gwas-database
by jaechang-hits
"NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published genome-wide association studies. Query studies, associations, variants, traits, genes, and summary statistics. Build polygenic risk score candidates, analyze variant pleiotropy, download summary statistics for Manhattan plots. No authentication required."
pyhealth
by jaechang-hits
"PyHealth is a Python library for healthcare machine learning. Build clinical prediction models from EHR (Electronic Health Record) data: process MIMIC-III/IV, eICU, and OMOP-CDM datasets, encode medical codes (ICD, ATC, NDC), construct patient-level datasets, and train models (Transformer, RETAIN, GRASP, MedBERT) for tasks including mortality prediction, drug recommendation, readmission, and diagnosis prediction. Alternatives: FIDDLE (EHR preprocessing only), clinical-longformer (NLP on clinical notes only), ehr-ml (EHR embedding only)."
biopython-sequence-analysis
by jaechang-hits
"Biopython toolkit for sequence analysis workflows: parse FASTA/FASTQ/GenBank/GFF with SeqIO, query NCBI databases via Entrez (esearch/efetch/elink), run remote and local BLAST with result parsing, perform pairwise and multiple sequence alignment (PairwiseAligner, MUSCLE/ClustalW), and build/visualize phylogenetic trees (Phylo module). Use for gene family studies, phylogenomics, comparative genomics, and programmatic NCBI pipelines. For PCR design, restriction digestion, and cloning workflows use biopython-molecular-biology; for SAM/BAM alignments use pysam."
cbioportal-database
by jaechang-hits
"Access TCGA and other cancer genomics datasets via cBioPortal REST API. Retrieve somatic mutations, copy number alterations, gene expression profiles, and clinical data (survival, stage, treatment) for thousands of cancer studies. Use for tumor mutation burden analysis, oncoprint queries, and survival analysis. For population variant frequencies use gnomad-database; for drug-gene interactions use dgidb-database."
post-trade-compliance
by JoelLewis
"Post-trade compliance and surveillance: trade surveillance, pattern detection, best execution review, allocation fairness, exception-based monitoring, and regulatory reporting triggers."
playwright-ux-ui-capture
by raphaelmansuy
Capture EdgeQuake WebUI routes with Playwright and write artifacts immediately (screenshots + per-page request JSON + capture index). Use when adding/updating Playwright E2E capture specs or when asked to automate UI screenshot collection.
prompt-enhancer
by sammcj
Knowledge for transforming poor or overly simple user prompts with expert-level framing. Triggers include: user explicitly asking to improve/refine/rewrite their prompt or user requesting help framing a request for another AI system.
apply-mantel-styles
by sammcj
Provides guidelines for applying Mantel's brand styles to diagrams and frontend components. Use when asked to create visuals that need to align with Mantel's branding.
piper-tts-training
by sammcj
Train custom TTS voices for Piper (ONNX format) using fine-tuning or from-scratch approaches. Use when creating new synthetic voices, fine-tuning existing Piper checkpoints, preparing audio datasets for TTS training, or deploying voice models to devices like Raspberry Pi or Home Assistant. Covers dataset preparation, Whisper-based validation, training configuration, and ONNX export.
ios-simulator-skill
by onejs
21 production-ready scripts for iOS app testing, building, and automation. Provides semantic UI navigation, build automation, accessibility testing, and simulator lifecycle management. Optimized for AI agents with minimal token output.
claude-settings-audit
by getsentry
Analyze a repository to generate recommended Claude Code settings.json permissions. Use when setting up a new project, auditing existing settings, or determining which read-only bash commands to allow. Detects tech stack, build tools, and monorepo structure.
database-testing
by proffesor-for-testing
"Database schema validation, data integrity testing, migration testing, transaction isolation, and query performance. Use when testing data persistence, ensuring referential integrity, or validating database migrations."