Skill catalog

Analyze or explore a codebase (remote or local repository) by packing it with the Repomix CLI, then reading and searching the generated output. Use when the user wants a high-level understanding of an unfamiliar or larg…

Build ETL pipelines and analytics dashboards for Harvard Art Museums API data using Python, SQL, and Streamlit

Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.

End-to-end data engineering and analytics application using Harvard Art Museums API with ETL pipelines, SQL analytics, and Streamlit visualization

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Query live Pyroscope profiles with profilecli, analyze them with pprof, and correlate hot functions with checked-out source code. Use when the user asks to investigate a service with a configured Pyroscope server, profi…

Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event scheduling, resource queues, interrupts, monitoring, independent replications, warm-up, and reproducible o…

Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protein annotation, pathway retrieval, chemical identifier mapping, and int…

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-to…

Load a sharded, on-disk dataset (sharded .npy, Parquet/Arrow, raw binary, sharded HDF5, custom layouts) into a distributed cuPyNumeric ndarray via a manual partition + leaf @task launch with CPU/OMP/GPU variants. Use wh…

Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structures, G2P residue annotations, enrichment analysis, OpenTargets, COSMIC…

Read datasheets and technical PDFs with `pcb scan`.

CDF Data Modeling limits: concurrency (429s), pagination, batching, search vs filter, QueuedTaskRunner, and the cap on LLM calls over query results (5 default, 50 max, cached). Triggers: DMS limits, 429, pagination, nex…

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h…

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astron…

Used for extracting selected metadata from one DICOM file and flagging standard-tag PHI presence. Not for anonymization or clinical use.

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugins, frames, private elements, JSON, and bounded de-identification r…

Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source…

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, paral…

Use people-search aggregators and primary public records to find addresses, phone numbers, relatives, age and background on a person, and to audit and remove your own exposure. Covers Spokeo, BeenVerified, Whitepages, T…

Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned visualizations, and file conversion. Use for larger-than-RAM HDF5, Arrow, CSV, or Parquet analysis, virtual…

Query and analyze Logfire telemetry data — traces, logs, spans, metrics, summaries, and SQL results. Use this skill when the user asks to "query logfire", "search traces", "find logs", "query data", "search spans", "loo…

Reconstruct data structures by analyzing memory access patterns across functions

Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking, compatible Dask execution, sparse…

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualizat…

Build ETL pipelines and analytics dashboards using Harvard Art Museums API data with Python, SQL, and Streamlit

End-to-end data engineering and analytics application for Harvard Art Museums API with ETL pipelines, SQL analytics, and Streamlit visualization

Queries and downloads public cancer imaging data from NCI Imaging Data Commons. Supports IDC collection discovery, DICOM access, radiology (CT, MR, PET) and pathology AI datasets, metadata SQL, visualization, licensing,…

Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry sensitivity, electronic-structure I/O, and bounded Materials Project q…

Provides data-retrieval best practices, tool selection guidance, and performant SQL query syntax for BigQuery telemetry across INFORMATION_SCHEMA, Cloud Monitoring, and the REST API. Use when the telemetry to fetch is a…

Stores and queries chunked N-D scientific arrays with Zarr-Python 3, including codecs, sharding, S3/GCS storage, and NumPy/Dask/Xarray integration. Use for array layout, bounded I/O, format migration, or scientific meta…

Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability, and complexity. Use when code imports neurokit2 or nee…

Read and write large cuPyNumeric arrays to HDF5 with Legate's parallel, distributed HDF5 I/O (legate.io.hdf5: to_file, from_file, from_file_batched). Use when a developer needs to save a cuPyNumeric array to an .h5/.hdf…

Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM referen…

Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for systems biology and meta…

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and cha…

Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy event extraction, multi-dataset files, table export, and FCS 3.…

Provides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits, evaluator metrics, benchmark groups, and bounded molecular-oracle scoring. Use when working with TDC…

Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts. Fits deterministic or dynamical models, examines gene phase portraits, builds velocity graphs, estimates relative latent time…

Queries the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auct…

Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage, and workflow integrati…

Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity…

Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and the CLI.

Extracts and preprocesses whole-slide histology image tiles with Histolab. Use for WSI inspection, tissue masks, random/grid/score-based tile extraction, H&E stain normalization, and tile dataset preparation. For multip…

Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data. Use for coordinate-aware genomi…

Analyzes Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and…

Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex L…

Best practices and guidelines for working with Postgres. Covers schema design, indexing strategies, query optimization, migrations, and common pitfalls. Use when writing SQL, designing database schemas, optimizing queri…

Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export l…