Processing
Data transformation and parsing
toon
by knoopx
Converts JSON to compact TOON format for reduced token usage. Use when inspecting JSON APIs, processing large JSON payloads, or reducing token costs when sending data to LLMs.
hyva-create-module
by hyva-themes
Create a new Magento 2 module in app/code/. This skill should be used when the user wants to create a module, scaffold a new module, generate module boilerplate, or set up a custom module. It handles registration.php, composer.json, module.xml generation with configurable dependencies. Trigger phrases include "create module", "new module", "scaffold module", "generate module".
openspec-archive-change
by PBH-BTN
Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.
session-investigator
by evalstate
Investigate fast-agent session and history files to diagnose issues. Use when a session ended unexpectedly, when debugging tool loops, when correlating sub-agent traces with main sessions, or when analyzing conversation flow and timing. Covers session.json metadata, history JSON format, message structure, tool call/result correlation, and common failure patterns.
novel-master
by bbroot
出版级中文长篇小说全流程创作技能包。当用户要求写小说、创作故事、分章节写作、连续剧情、章节悬念、长篇小说时触发。覆盖从世界观设定、人物塑造、大纲规划、分章撰写到伏笔管理、质量控制的全链路。
openspec-ff-change
by PBH-BTN
Fast-forward through OpenSpec artifact creation. Use when the user wants to quickly create all artifacts needed for implementation without stepping through each one individually.
rev-idapython
by P4nda0s
IDAPython and IDALib script reference for reverse engineering. Activate when the user needs to write IDAPython scripts in IDA, use IDALib for headless analysis, operate on IDB databases, debug with IDA, manipulate memory/registers, traverse functions/blocks/instructions, work with Hex-Rays decompiler API, handle obfuscation, or batch-process binaries.
gene-database
by jaechang-hits
"Query NCBI Gene via E-utilities for curated gene records across 1M+ taxa. Retrieve official gene symbols, aliases, RefSeq accessions, summary descriptions, genomic coordinates, GO annotations, and interaction data. Use for gene ID resolution, cross-species queries, and gene function summaries. For sequence retrieval use Ensembl; for expression data use geo-database."
planning-under-uncertainty
by RefoundAI
Help users plan products and strategy when outcomes are unpredictable. Use when someone is dealing with ambiguous timelines, building in fast-moving markets, planning AI/ML projects, or asking how to make commitments when they don't know what will happen.
organizational-transformation
by RefoundAI
Help users transform organizations toward modern product practices. Use when someone is trying to shift from feature teams to product teams, introduce empowered teams, modernize legacy processes, or drive cultural change in how product is built.
flowio-flow-cytometry
by jaechang-hits
"Parse and create FCS (Flow Cytometry Standard) files v2.0-3.1. Read event data as NumPy arrays, extract channel metadata, handle multi-dataset files, export to CSV/FCS. For advanced gating and compensation use FlowKit."
encode-database
by jaechang-hits
"Query the ENCODE Portal REST API for regulatory genomics data: TF ChIP-seq experiments, ATAC-seq/DNase-seq accessibility peaks, histone mark tracks, and RNA-seq datasets across 1000+ cell types and tissues. Search experiments by assay, biosample, or target protein; download BED/bigWig files; retrieve candidate cis-regulatory elements (cCREs) from ENCODE SCREEN by genomic region or gene. Use for finding regulatory tracks to annotate variants, identifying open chromatin in a cell type of interest, and downloading peak files for ChIP-seq or ATAC-seq analysis. For regulatory variant scoring use regulomedb-database; for GWAS associations use gwas-database."
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."
imaging-data-commons
by jaechang-hits
"Query NCI Imaging Data Commons (IDC) for cancer radiology and pathology imaging datasets hosted on Google Cloud. Search DICOM collections by modality, anatomical site, cancer type, or collection name. Download images via Google Cloud Storage or IDAT tool. 50TB+ of publicly accessible DICOM images. Requires Google Cloud account for large downloads; small queries work without billing. For local DICOM processing use pydicom-medical-imaging; for whole-slide pathology use histolab."
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."
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."
geo-database
by jaechang-hits
"Query NCBI Gene Expression Omnibus (GEO) for gene expression datasets and sample metadata via GEOparse Python library and E-utilities. Search datasets by keyword/organism/platform, download GSE series matrices, parse GPL platform annotations, extract GSM sample metadata, and load expression matrices into pandas. For single-cell data use cellxgene-census; for programmatic multi-DB access use gget-genomic-databases."
omero-integration
by jaechang-hits
"OMERO is an open-source platform for biological image data management. Use the omero-py Python client to connect to an OMERO server, search and retrieve images as numpy arrays, annotate images with tags and key-value pairs, manage ROIs, and integrate OMERO image data into downstream analysis pipelines — all programmatically without the OMERO desktop GUI."
pymc-bayesian-modeling
by jaechang-hits
"Bayesian modeling with PyMC 5. 8-step workflow: define model, set priors, define likelihood, sample (NUTS/ADVI), diagnose (R-hat, ESS, divergences), interpret posteriors, compare models (LOO/WAIC), predict. Hierarchical, logistic, GP model variants. Prior/posterior predictive checks."
bcftools-variant-manipulation
by jaechang-hits
"Command-line toolkit for VCF/BCF variant file manipulation. Filter, merge, annotate, query, normalize, and compute statistics on variant call files. Essential for post-variant-calling pipelines: quality filtering, multi-sample merging, rsID annotation, and genotype extraction. Companion to samtools in the HTSlib ecosystem. Use GATK instead for complex indel realignment during variant calling; use VCFtools instead for population genetics statistics."
anndata-data-structure
by jaechang-hits
"Annotated data matrices for single-cell genomics. AnnData stores expression data (X) with observation metadata (obs), variable metadata (var), layers, embeddings (obsm/varm), graphs (obsp/varp), and unstructured data (uns). Use for .h5ad/.zarr file handling, dataset concatenation, and scverse ecosystem integration. For analysis workflows use scanpy; for probabilistic models use scvi-tools."
schemantic
by genkit-ai
Instructions and guidelines for using the Schemantic library for type-safe data classes and schemas in Dart.
archs4-database
by jaechang-hits
"Query uniformly processed RNA-seq gene expression profiles, tissue-specific expression patterns, and co-expression networks from the ARCHS4 database REST API. Retrieve z-score normalized expression across 1M+ human and mouse samples, find co-expressed genes, search samples by metadata, and download HDF5 expression matrices. For variant-level population genetics use gnomad-database; for pathway enrichment from gene lists use gget-genomic-databases (Enrichr)."
clinical-decision-support-documents
by jaechang-hits
"Guidelines for generating clinical decision support (CDS) documents: patient cohort analyses (biomarker-stratified outcomes) and treatment recommendation reports (GRADE-graded evidence). Covers document structure, executive summary design, evidence grading (GRADE 1A–2C), statistical reporting (HR, CI, survival), and biomarker integration. Use when creating pharmaceutical research documents, clinical guidelines, or regulatory submissions."