skillquarium

Project-wide code coverage and CRAP (Change Risk Anti-Patterns) score analysis for .NET projects. Calculates CRAP scores per method and surfaces risk hotspots — complex code with low coverage that is dangerous to modify. Use to diagnose why coverage is stuck or plateaued, identify what methods block improvement, or get project-wide coverage analysis with risk ranking. USE FOR: coverage stuck, coverage plateau, can't increase coverage, what's blocking coverage, coverage gap, CRAP scores, risk hotspots, where to add tests, coverage analysis, coverage report. DO NOT USE FOR: targeted single-method CRAP analysis (use crap-score); auditing test code for coverage-touching or other anti-patterns (use test-anti-patterns); writing tests; running tests (use run-tests). Requires or produces coverage (Cobertura) and CRAP metrics.

Role-based multi-agent orchestration framework for building "Crews" of collaborating LLM agents (each with a role, goal, backstory, and optional tools) that execute sequential or hierarchical task pipelines, plus event-driven "Flows" for precise, single-LLM-call orchestration. Use when composing specialized agents (e.g. a research agent + an analysis agent + a writer agent) into a declarative pipeline for complex multi-step tasks like automated literature review or multi-agent research workflows. Distinct from LangGraph's explicit state-machine graphs and smolagents' minimal tool-calling loop — CrewAI is standalone (no LangChain dependency) and expresses orchestration as roles and delegated tasks rather than a graph or a single ReAct loop.

Adapter, primer, and poly-A/T trimming for high-throughput sequencing reads (FASTQ/FASTA). Use for ATAC-seq (Nextera adapter removal), ChIP-seq/CUT&RUN, small RNA-seq (preserving reads as short as ~18 nt), and amplicon/primer trimming where exact or linked adapter sequences matter more than fastp's heuristic auto-detection. Covers 3'/5'/linked adapters, IUPAC wildcards, paired-end synchronization, quality/length filtering, and demultiplexing by barcode.

Data Version Control (DVC) for tracking large datasets/models with Git-like semantics, defining reproducible data/ML pipelines (dvc.yaml stages that only re-run when their inputs change), and lightweight experiment tracking without a server. Use when large files (VCF/BAM/FASTQ, reference genomes, model weights) can't go in Git, when you need Make/Snakemake-style selective re-execution driven by data, or when comparing many training runs locally before promoting one. Pairs with Git (code), cloud object storage (data), and Snakemake/Nextflow (compute graph).

Fast Python I/O for BigWig (continuous genome signal) and BigBed (interval annotation) files via libBigWig. Use for random-access signal queries at specific genomic coordinates (bw.values, bw.stats), computing per-region summary statistics (mean/max/coverage) over a BED file of regions, writing custom BigWig tracks from numpy arrays, and loading ChIP-seq/ATAC-seq/RNA-seq/methylation coverage tracks (e.g. produced by deeptools bamCoverage) into pandas/numpy for downstream analysis or ML feature extraction. Complements deeptools (which generates BigWig files) and chip-seq/atac-seq workflows.

Distributed Python compute with Ray — @ray.remote tasks/actors for cluster-scale parallelism, Ray Data for large-batch preprocessing, Ray Train for distributed model training (DDP/FSDP/DeepSpeed), Ray Tune for scalable hyperparameter search, and Ray Serve for model serving. Use when scaling a Python workload (docking screens, million-cell atlas preprocessing, hyperparameter sweeps, multi-GPU training) from a laptop to a multi-node cluster with minimal code changes. Ray Tune can use optuna as a search algorithm; Ray Train wraps pytorch-lightning-style training loops.

MinHash/FracMinHash sketching for alignment-free comparison of genomes and metagenomes. Use for fast all-vs-all genome similarity and ANI estimation across thousands of genomes without alignment, taxonomic classification of metagenomes against GTDB/NCBI reference databases (sourmash gather/tax), and sequencing-cohort QC (contamination or duplicate detection). Complements upstream assembly/QC pipelines (snakemake-workflow-engine, nextflow) and feeds downstream phylogenetics; distinct from alignment-based tools like BLAST or mash-style exact-num MinHash by supporting scaled (FracMinHash) sketches that compare well across very different dataset sizes.

Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models (Transformer, RETAIN, GAMENet, SafeDrug, MICRON, StageNet, AdaCare, CNN/RNN/MLP), training with the PyHealth Trainer, computing clinical metrics, and using medical code utilities (ICD/ATC/NDC/RxNorm lookup and cross-mapping). Use this skill whenever the user mentions PyHealth, MIMIC, eICU, OMOP, EHR modeling, clinical prediction, drug recommendation, sleep staging, medical code mapping, ICD/ATC codes, or any healthcare ML pipeline that fits the dataset → task → model → trainer → metrics pattern, even if "PyHealth" isn't named explicitly.

Query AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".

Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.

End-to-end ML phylogenetic tree inference — MSA, trimming, ModelFinder, IQ-TREE2/RAxML-NG.

IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.

Build, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning.

Genome, transcriptome, and protein completeness assessment via BUSCO v6. Agentic lineage routing from organism description, all three BUSCO modes, auto-lineage support, and full demo mode without the BUSCO binary.

Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated workloads (training, fine-tuning, inference), serving web endpoints, scheduling batch jobs, or scaling Python code to cloud containers with the Modal SDK.

Query 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 H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.

Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival library.

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.

Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

Use this skill when the user wants a .pptx with smooth cross-slide animation — PowerPoint Morph transitions, Keynote-style continuous motion, shapes that grow / move / rotate as the slide advances. Trigger on: 'morph', 'morph transition', 'smooth transition', 'continuous animation across slides', 'Keynote-style transition', 'animated slide sequence', 'shape continuity across slides'. Output is a single .pptx. This skill is a scene layer on top of officecli-pptx — inherits every pptx v2 rule (visual floor, grid, palettes, connector canon, Delivery Gate 1–5a). DO NOT invoke for a generic deck, pitch deck, or board review without cross-slide motion — route those to officecli-pptx base or officecli-pitch-deck.

Use this skill to build academic-style .docx output: journal / conference / thesis chapters carrying formal citation style (APA, Chicago, IEEE, MLA), numbered equations, figure & table cross-references, footnotes/endnotes, bibliography, or multi-column journal layout. Trigger on: 'research paper', 'journal paper', 'conference paper', 'manuscript', 'thesis', 'APA', 'MLA', 'Chicago', 'IEEE two-column', 'bibliography', 'hanging indent', 'citation style', 'abstract + keywords', 'equation numbering', 'cross-reference', paper with footnotes/endnotes. Output is a single .docx.

Use this skill to build a multi-element Excel dashboard — Dashboard sheet on open, multiple formula-driven KPI cards, multiple charts, sparklines, and conditional formatting — from CSV or tabular input. Trigger on: 'dashboard', 'KPI dashboard', 'analytics dashboard', 'executive dashboard', 'metrics dashboard', 'CSV to dashboard', 'data visualization'. Output is a single .xlsx. Scene-layer on officecli-xlsx: inherits every xlsx hard rule. DO NOT invoke for: a single budget tracker / one-sheet CSV-with-formatting (use xlsx), a 3-statement / DCF / LBO financial model (use financial-model), a weekly report with ≤ 1 chart and < 10 rows (use xlsx).

Use this skill any time a .docx file is involved -- as input, output, or both. This includes: creating Word documents, reports, letters, memos, or proposals; reading, parsing, or extracting text from any .docx file; editing, modifying, or updating existing documents; working with templates, tracked changes, comments, headers/footers, or tables of contents. Trigger whenever the user mentions 'Word doc', 'document', 'report', 'letter', 'memo', or references a .docx filename.

Use this skill when the user wants to build a financial model — 3-statement model, DCF valuation, LBO, SaaS unit economics, sensitivity / scenario analysis, debt schedule, or fundraising projections — in Excel. Trigger on: 'financial model', '3-statement model', 'P&L + BS + CF', 'DCF', 'WACC', 'NPV', 'terminal value', 'LBO', 'debt schedule', 'cash sweep', 'MOIC', 'IRR / XIRR', 'sensitivity table', 'scenario analysis', 'ARR model', 'unit economics', 'CAC / LTV', 'cap table forecast'. Output is a single formula-driven .xlsx. This skill is a scene layer on top of officecli-xlsx — it inherits every xlsx v2 rule (4-color code, visual floor, number formats, cache-drift, Known Issues, Delivery Gate minimum cycle). DO NOT invoke for a simple budget tracker, CSV dump, or operational KPI sheet — route those to officecli-xlsx base.

Use this skill when the user is building a fundraising / investor pitch deck — seed, Series A / B / C, convertible note, SAFE round, strategic raise. Trigger on: 'pitch deck', 'investor deck', 'Series A deck', 'Series B deck', 'Series C deck', 'fundraising deck', 'seed pitch', 'VC deck', 'raising capital', 'term sheet presentation'. Output is a single .pptx. This skill is a scene layer on top of officecli-pptx — inherits every pptx v2 rule (visual floor, grid, palettes, connector canon, Delivery Gate). DO NOT invoke for a generic board review, sales deck, all-hands, or product launch — route those to officecli-pptx base.

Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings. Pipeline: sequence → MFE → partition function and pair-probability matrix → dot-bracket → duplex. Use for siRNA/sgRNA targeting, ribozyme design, RNA accessibility. Use RNAfold CLI for batch use without Python.

How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.

Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word "Nextflow", and for authoring nf-core-compliant pipelines, modules, configs, and linting.

PyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets. Use when working with torch_geometric, not for general NetworkX analytics or non-graph PyTorch models.

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

A Just-In-Time (JIT) compiler for Python that translates a subset of Python and NumPy code into fast machine code. Developed by Anaconda, Inc. Highly effective for accelerating loops, custom mathematical functions, and complex numerical algorithms. Use for @njit, @vectorize, prange, cuda.jit, numba.typed, JIT compilation, parallel loops, GPU acceleration with CUDA, Monte Carlo simulations, numerical algorithms, and high-performance Python computing.