Data & Reproduction

aeon

Aeon is a scikit-learn compatible Python toolkit for time series machine learning. It provides state-of-the-art algorithms for classificatio…

agent-browser

Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…

arxiv-database

This skill provides Python tools for searching and retrieving preprints from arXiv.org via its public Atom API. It supports keyword search,…

Astropy

Astropy is the core Python package for astronomy, providing essential functionality for astronomical research and data analysis. Use astropy…

bayesian-optimizer

Bayesian optimization for experimental design and hyperparameter tuning in biomedical research.

Benchling Integration

Benchling is a cloud platform for life sciences R&D. Access registry entities (DNA, proteins), inventory, electronic lab notebooks, and work…

bgpt-paper-search

BGPT is a remote MCP server that searches a curated database of scientific papers built from raw experimental data extracted from full-text…

bio-alignment-files-bam-statistics

Compute alignment statistics: flagstat, idxstats, coverage depth.

bio-alignment-msa-statistics

Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when com…

bio-blast-searches

Run BLAST searches against local or remote databases for sequence homology.

bio-causal-genomics-colocalization-analysis

Colocali.

bio-causal-genomics-fine-mapping

Fine-mapping narrows GWAS association signals to identify likely causal variants. Key outputs: - **PIP** (Posterior Inclusion Probability) -…

bio-causal-genomics-mediation-analysis

Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expre…

bio-causal-genomics-mendelian-randomization

Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR…

bio-causal-genomics-pleiotropy-detection

Hori.

bio-chipseq-differential-binding

Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples.…

bio-chipseq-peak-annotation

Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. F…

bio-chipseq-visualization

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal a…

bio-clinical-databases-polygenic-risk

Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genom…

bio-consensus-sequences

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific refer…

bio-copy-number-cnv-visualization

Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or oth…

bio-crispr-screens-base-editing-analysis

Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies. Use when quantifying…

bio-crispr-screens-batch-correction

Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use…

bio-crispr-screens-crispresso-editing

CRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports. Use…

bio-crispr-screens-hit-calling

Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and re…

bio-crispr-screens-jacks-analysis

JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR…

bio-crispr-screens-library-design

CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designi…

bio-crispr-screens-mageck-analysis

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene rankin…

bio-crispr-screens-screen-qc

Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recov…

bio-data-visualization-circos-plots

Circular genome visualization with Circos or pycirclize.

bio-data-visualization-genome-tracks

Multi-panel genome track plots with pyGenomeTracks.

bio-data-visualization-ggplot2-fundamentals

R ggplot2 for publication-quality genomics and omics figures.

bio-data-visualization-heatmaps-clustering

Hierarchical clustering heatmaps with ComplexHeatmap or seaborn.

bio-data-visualization-interactive-visualization

Interactive omics visualizations with Plotly, Bokeh, or shiny.

bio-data-visualization-multipanel-figures

Compose multipanel publication figures with cowplot or patchwork.

bio-data-visualization-specialized-omics-plots

Specialized plots: lollipop (mutations), circomap, oncoprint.

bio-data-visualization-upset-plots

UpSet plots for multi-set intersection visualization.

bio-data-visualization-volcano-customization

Customized volcano plots with ggplot2 or matplotlib for DE results.

bio-de-edger-basics

Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-tes…

bio-de-visualization

Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample di…

bio-entrez-link

Retrieve linked records across NCBI Entrez databases.

bio-epidemiological-genomics-amr-surveillance

Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends an…

bio-epidemiological-genomics-pathogen-typing

Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst…

bio-epidemiological-genomics-phylodynamics

Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times…

bio-epidemiological-genomics-transmission-inference

Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimat…

bio-epidemiological-genomics-variant-surveillance

Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify eme…

bio-epitranscriptomics-modification-visualization

Visualize RNA modification profiles and metagene plots.

bio-experimental-design-power-analysis

Statistical power analysis for detecting differential signals.

bio-flow-cytometry-differential-analysis

Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use whe…

bio-gatk-variant-calling

Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint geno…

bio-genome-engineering-base-editing-design

Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positio…

bio-genome-engineering-grna-design

Design guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity usin…

bio-genome-engineering-hdr-template-design

Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimi…

bio-genome-engineering-off-target-prediction

Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and…

bio-genome-engineering-prime-editing-design

Design pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modificat…

bio-hi-c-analysis-contact-pairs

Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequ…

bio-hi-c-analysis-hic-differential

Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical sig…

bio-hi-c-analysis-hic-visualization

Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virt…

bio-imaging-mass-cytometry-spatial-analysis

Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Us…

bio-local-blast

Set up and run BLAST+ locally with custom databases.

bio-longread-qc

Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality…

bio-metabolomics-normalization-qc

Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods.…

bio-metabolomics-statistical-analysis

Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery. Use when…

bio-metagenomics-kraken

Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing in…

bio-metagenomics-visualization

Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plot…

bio-methylation-methylkit

DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical…

bio-pathway-enrichment-visualization

Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results.…

bio-pathway-go-enrichment

Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list…

bio-pathway-kegg-pathways

KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling p…

bio-pathway-reactome

Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway databas…

bio-population-genetics-scikit-allel-analysis

Population genetics analysis with scikit-allel: diversity, Fst, haplotypes.

bio-proteomics-differential-abundance

Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correc…

bio-reporting-figure-export

Export publication-quality figures in PDF/SVG/TIFF at specified DPI.

bio-reporting-rmarkdown-reports

Render Rmarkdown reports with integrated plots and statistics.

bio-sashimi-plots

Creates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot. Visualizes differential…

bio-sequence-statistics

Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets,…

bio-single-cell-cell-communication

Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. Use…

bio-single-cell-metabolite-communication

Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types. Predict metabolite…

bio-spatial-transcriptomics-spatial-communication

Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular signaling,…

bio-spatial-transcriptomics-spatial-statistics

Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occur…

bio-spatial-transcriptomics-spatial-visualization

Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlai…

bio-tcr-bcr-analysis-repertoire-visualization

Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network gra…

bio-vcf-statistics

Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality,…

bio-workflows-crispr-screen-pipeline

CRISPR screen: guide counting → MAGeCK → hit calling → visualization.

bio-workflows-expression-to-pathways

End-to-end workflow from differential expression to GO/KEGG/Reactome enrichment and pathway visualization.

bio-workflows-imc-pipeline

Imaging mass cytometry: segmentation → phenotyping → spatial analysis.

bio-workflows-metabolic-modeling-pipeline

Metabolic model reconstruction → FBA → simulation → visualization.

bio-workflows-metabolomics-pipeline

LC-MS/GC-MS: preprocessing → annotation → statistical analysis.

bioinformatics-singlecell

General single-cell bioinformatics: clustering, trajectory, cell communication.

biomedical-data-analysis

Comprehensive biomedical data analysis: statistics, visualization, and interpretation.

BioServices

BioServices is a Python package providing programmatic access to approximately 40 bioinformatics web services and databases. Retrieve biolog…

bulk-rna-seq-deseq2-analysis-with-omicverse

Use this skill when a user wants to reproduce the DESeq2 workflow showcased in [`t_deseq2.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/…

bulk-rna-seq-differential-expression-with-omicverse

Follow this skill to run the end-to-end differential expression (DEG) workflow showcased in [`t_deg.ipynb`](../../omicverse_guide/docs/Tutor…

care-coordination

Care coordination agent: multi-disciplinary team communication and care plan management.

Citation Management

Manage citations systematically throughout the research and writing process. This skill provides tools and strategies for searching academic…

Clinical Decision Support

Generate professional clinical decision support (CDS) documents for pharmaceutical companies, clinical researchers, and medical decision-mak…

Clinical Reports

Clinical report writing is the process of documenting medical information with precision, accuracy, and compliance with regulatory standards…

clinicaltrials-database

ClinicalTrials.gov is a comprehensive registry of clinical studies conducted worldwide, maintained by the U.S. National Library of Medicine.…

convergence-study

Spatial and temporal convergence analysis with Richardson extrapolation and Grid Convergence Index (GCI) for solution verification.

Dask

Dask is a Python library for parallel and distributed computing that enables three critical capabilities: - **Larger-than-memory execution**…

Data Commons

Use the `idc-index` Python package to query and download public cancer imaging data from the National Cancer Institute Imaging Data Commons…

data-stats-analysis

This skill enables you to perform rigorous statistical analyses including t-tests, ANOVA, correlation analysis, hypothesis testing, and mult…

data-transform

This skill enables you to perform comprehensive data transformations including cleaning, normali.

data-visualization-biomedical

Biomedical-specific data visualization: clinical trial plots, survival curves, forest plots.

data-visualization-expert

Expert data visualization for complex scientific and clinical datasets.

data-viz-plots

This skill enables you to create professional scientific visuali.

datacommons-client

Provides comprehensive access to the Data Commons Python API v2 for querying statistical observations, exploring the knowledge graph, and re…

deepTools

deepTools is a comprehensive suite of Python command-line tools designed for processing and analy.

Denario

Denario is a multiagent AI system designed to automate scientific research workflows from initial data analysis through publication-ready ma…

dhdna-profiler

A structured system for extracting the cognitive fingerprint of any text's author. Based on the Digital Human DNA (DHDNA) framework — the th…

differentiation-schemes

Select and apply numerical differentiation schemes for PDE/ODE discretization. Use when choosing finite difference/volume/spectral schemes,…

DNAnexus Integration

DNAnexus is a cloud platform for biomedical data analysis and genomics. Build and deploy apps/applets, manage data objects, run workflows, a…

docx

A.docx file is a.

equity-scorer

Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity S…

etetoolkit

ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analy.

Exploratory Data Analysis

Perform comprehensive exploratory data analysis (EDA) on scientific data files across multiple domains. This skill provides automated file t…

find-skills

Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can…

FluidSim

FluidSim is an object-oriented Python framework for high-performance computational fluid dynamics (CFD) simulations. It provides solvers for…

FRED Economic Data

Access comprehensive economic data through FRED (Federal Reserve Economic Data), a database maintained by the Federal Reserve Bank of St. Lo…

Generate Image

Generate and edit high-quality images using OpenRouter's image generation models including FLUX.2 Pro and Gemini 3.1 Flash Image Preview.

geomaster

Comprehensive geospatial science skill covering GIS, remote sensing, spatial analysis, and ML for Earth observation across 70+ topics with 5…

GeoPandas

GeoPandas extends pandas to enable spatial operations on geometric types. It combines the capabilities of pandas and shapely for geospatial…

gnomad-database

The Genome Aggregation Database (gnomAD) is the largest publicly available collection of human genetic variation, aggregated from large-scal…

gtex-database

The Genotype-Tissue Expression (GTEx) project provides a comprehensive resource for studying tissue-specific gene expression and genetic reg…

gwas-database

The GWAS Catalog is a comprehensive repository of published genome-wide association studies maintained by the National Human Genome Research…

hedgefundmonitor

Free, open REST API from the U.S. Office of Financial Research (OFR) providing aggregated hedge fund time series data. No API key or registr…

HypoGeniC

Hypogenic provides automated hypothesis generation and testing using large language models to accelerate scientific discovery. The framework…

infographics

Infographics are visual representations of information, data, or knowledge designed to present complex content quickly and clearly. **This s…

instrument-data-to-allotrope

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this…

KEGG

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a comprehensive bioinformatics resource for biological pathway analysis and molecular inte…

labarchive-integration

LabArchives is an electronic lab notebook platform for research documentation and data management. Access notebooks, manage entries and atta…

LaminDB

LaminDB is an open-source data framework for biology designed to make data queryable, traceable, reproducible, and FAIR (Findable, Accessibl…

LatchBio Integration

Latch is a Python framework for building and deploying bioinformatics workflows as serverless pipelines. Built on Flyte, create workflows wi…

LaTeX Posters

Research posters are a critical medium for scientific communication at conferences, symposia, and academic events. This skill provides compr…

linear-solvers

Select and configure linear solvers for systems Ax=b in dense and sparse problems. Use when choosing direct vs iterative methods, diagnosing…

lobster-bioinformatics

Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and…

markdown-mermaid-writing

This skill teaches you — and enforces a standard for — creating scientific documentation using **markdown with embedded Mermaid diagrams as…

Market Research Reports

Market research reports are comprehensive strategic documents that analy.

matlab

MATLAB is a numerical computing environment optimized for matrix operations and scientific computing. GNU Octave is a free, open-source alte…

Matplotlib

Matplotlib is Python's foundational visuali.

monarch-database

The Monarch Initiative (https://monarchinitiative.org/) is a multi-species integrated knowledgebase that links genes, diseases, and phenotyp…

multi-search-engine

Multi search engine integration with 17 engines (8 CN + 9 Global). Supports advanced search operators, time filters, site search, privacy en…

NetworkX

NetworkX is a Python package for creating, manipulating, and analy.

nonlinear-solvers

Select and configure nonlinear solvers for f(x)=0 or min F(x). Use for Newton methods, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson accele…

numerical-integration

Select and configure time integration methods for ODE/PDE simulations. Use when choosing explicit/implicit schemes, setting error tolerances…

numerical-stability

Analyze and enforce numerical stability for time-dependent PDE simulations. Use when selecting time steps, choosing explicit/implicit scheme…

ontology-explorer

Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Use when exploring an ontology like CMSO,…

ontology-mapper

Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties. Supports any ontology registere…

ontology-validator

Validate material sample annotations and data structures against ontology constraints. Use when checking if CMSO annotations are correct, ve…

OpenAlex

OpenAlex is a comprehensive open catalog of 240M+ scholarly works, authors, institutions, topics, sources, publishers, and funders. This ski…

Opentrons Integration

Opentrons is a Python-based lab automation platform for Flex and OT-2 robots. Write Protocol API v2 protocols for liquid handling, control h…

opentrons-protocol-agent

Opentrons liquid handler protocol design for automated lab workflows.

Paper-2-Web

This skill enables the transformation of academic papers into multiple promotional and presentation formats using the Paper2All autonomous p…

parameter-optimization

Explore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection. Use for calibrati…

pdf

This guide covers essential PDF processing operations using Python libraries and command-line tools. For advanced features, JavaScript libra…

Peer Review

Peer review is a systematic process for evaluating scientific manuscripts. Assess methodology, statistics, design, reproducibility, ethics,…

performance-profiling

Identify computational bottlenecks, analyze scaling behavior, estimate memory requirements, and receive optimization recommendations for any…

Perplexity Search

Perform AI-powered web searches using Perplexity models through LiteLLM and OpenRouter. Perplexity provides real-time, web-grounded answers…

Plotly

Python graphing library for creating interactive, publication-quality visualizations with 40+ chart types.

Polars

Polars is a lightning-fast DataFrame library for Python and Rust built on Apache Arrow. Work with Polars' expression-based API, la.

Polars

polars-bio is a high-performance Python library for genomic interval operations and bioinformatics file I/O, built on Polars, Apache Arrow,…

post-processing

Extract, analyze, and visualize simulation output data. Use for field extraction, time series analysis, line profiles, statistical summaries…

pptx

| Task | Guide | |------|-------| | Read/analyze content | `python -m markitdown presentation.pptx` | | Edit or create from template | Read…

PPTX Posters

**⚠️ USE THIS SKILL ONLY WHEN USER EXPLICITLY REQUESTS PPTX/POWERPOINT POSTER FORMAT.** For standard research posters, use the **latex-poste…

protocolsio-integration

Protocols.io is a comprehensive platform for developing, sharing, and managing scientific protocols. This skill provides complete integratio…

pubmed-search

Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or a…

PyDESeq2

PyDESeq2 is a Python implementation of DESeq2 for differential expression analysis with bulk RNA-seq data. Design and execute complete workf…

pydicom

Pydicom is a pure Python package for working with DICOM files, the standard format for medical imaging data. This skill provides guidance on…

PyLabRobot

PyLabRobot is a hardware-agnostic, pure Python Software Development Kit for automated and autonomous laboratories. Use this skill to control…

Pymatgen

Pymatgen is a comprehensive Python library for materials analysis that powers the Materials Project. Create, analy.

PyMC

PyMC is a Python library for Bayesian modeling and probabilistic programming. Build, fit, validate, and compare Bayesian models using PyMC's…

PyTorch Lightning

PyTorch Lightning is a deep learning framework that organi.

pyzotero

Pyzotero is a Python wrapper for the [Zotero API v3](https://www.zotero.org/support/dev/web_api/v3/start). Use it to programmatically manage…

Reactome

Reactome is a free, open-source, curated pathway database with 2,825+ human pathways. Query biological pathways, perform overrepresentation…

Research Grants

Research grant writing is the process of developing competitive funding proposals for federal agencies and foundations. Master agency-specif…

Research Lookup

This skill provides real-time research information lookup with **intelligent backend routing**: - **Parallel Chat API** (`core` model): Defa…

Scanpy

Scanpy is a scalable Python toolkit for analy.

Scholar Evaluation

Apply the ScholarEval framework to systematically evaluate scholarly and research work. This skill provides structured evaluation methodolog…

Scientific Critical Thinking

Critical thinking is a systematic process for evaluating scientific rigor. Assess methodology, experimental design, statistical validity, bi…

Scientific Schematics

Scientific schematics and diagrams transform complex concepts into clear visual representations for publication. **This skill uses Nano Bana…

Scientific Slides

Scientific presentations are a critical medium for communicating research, sharing findings, and engaging with academic and professional aud…

Scientific Visualization

Scientific visuali.

Scientific Writing

**This is the core skill for the deep research and writing tool**—combining AI-driven deep research with well-formatted written outputs. Eve…

scikit-bio

scikit-bio is a comprehensive Python library for working with biological data. Apply this skill for bioinformatics analyses spanning sequenc…

Seaborn

Seaborn is a Python visuali.

SHAP

SHAP is a unified approach to explain machine learning model outputs using Shapley values from cooperative game theory. This skill provides…

SimPy

SimPy is a process-based discrete-event simulation framework based on standard Python. Use SimPy to model systems where entities (customers,…

simulation-orchestrator

Orchestrate multi-simulation campaigns including parameter sweeps, batch jobs, and result aggregation. Use for running parameter studies, ma…

simulation-validator

Validate simulations before, during, and after execution. Use for pre-flight checks, runtime monitoring, post-run validation, diagnosing fai…

single-cell-cellphonedb-communication-mapping

Apply this skill when a user wants to quantify ligand–receptor communication between annotated single-cell populations and display the netwo…

single-cell-rna-qc

Performs quality control on single-cell RNA-seq data (.h5ad or.h5 files) using scverse best practices with MAD-based filtering and comprehen…

spatial-communication

spatial-communication.

spatial-statistics

spatial-statistics.

spatial-transcriptomics-tutorials-with-omicverse

Use this skill to navigate the spatial analysis tutorials located under [`Tutorials-space`](../../omicverse_guide/docs/Tutorials-space/). Th…

spatial-visualization

spatial-visualization.

Statistical Analysis

Statistical analysis is a systematic process for testing hypotheses and quantifying relationships. Conduct hypothesis tests (t-test, ANOVA,…

statsmodels

Statsmodels is Python's premier library for statistical modeling, providing tools for estimation, inference, and diagnostics across a wide r…

string-protein-interaction-analysis-with-omicverse

Invoke this skill when the user has a list of genes and wants to explore STRING protein–protein interactions via omicverse. The workflow mir…

SymPy

SymPy is a Python library for symbolic mathematics that enables exact computation using mathematical symbols rather than numerical approxima…

time-stepping

Plan and control time-step policies for simulations. Use when coupling CFL/physics limits with adaptive stepping, ramping initial transients…

timesfm-forecasting

TimesFM (Time Series Foundation Model) is a pretrained decoder-only foundation model developed by Google Research for time-series forecastin…

tooluniverse-cancer-variant-interpretation

Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) a…

tooluniverse-clinical-trial-matching

AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, pri…

tooluniverse-epigenomics

Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differe…

tooluniverse-gwas-finemapping

Genome-wide association studies (GWAS) identify genomic regions associated with traits, but linkage disequilibrium (LD) makes it difficult t…

tooluniverse-gwas-study-explorer

The GWAS Study Deep Dive & Meta-Analysis skill enables comprehensive comparison of genome-wide association studies (GWAS) for the same trait…

tooluniverse-image-analysis

Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantific…

tooluniverse-immunotherapy-response-prediction

Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, a…

tooluniverse-metabolomics-analysis

Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Processes LC-MS, GC-MS,…

tooluniverse-phylogenetics

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treen…

tooluniverse-polygenic-risk-score

**Use Cases:** - "Calculate my genetic risk for type 2 diabetes" - "Build a polygenic risk score for coronary artery disease" - "What's my g…

tooluniverse-precision-oncology

Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-appr…

tooluniverse-proteomics-analysis

Analyze mass spectrometry proteomics data including protein quantification, differential expression, post-translational modifications (PTMs)…

tooluniverse-rnaseq-deseq2

Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing…

tooluniverse-single-cell

Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMA…

tooluniverse-spatial-omics-analysis

Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations…

tooluniverse-statistical-modeling

Perform statistical modeling and regression analysis on biomedical datasets. Supports linear regression, logistic regression (binary/ordinal…

tooluniverse-variant-analysis

Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics qu…

ukb-navigator

Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

UMAP-learn

UMAP (Uniform Manifold Approximation and Projection) is a dimensionality reduction technique for visuali.

usfiscaldata

Free, open REST API from the U.S. Department of the Treasury for federal financial data. No API key or registration required.

Vaex

Vaex is a high-performance Python library designed for la.

vcf-annotator

Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.

vcf-statistics

vcf-statistics.

Venue Templates

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues, academic c…

virtual-lab-agent

Virtual lab agent for in silico experiment simulation and protocol optimization.

wikipedia-search

Search and fetch structured content from Wikipedia using the MediaWiki API for reliable, encyclopedic information.

writing

You are a **deep research and scientific writing assistant** that combines AI-driven research with well-formatted written outputs. Create hi…

xlsx

A user may ask you to create, edit, or analy.

XLSX

A user may ask you to create, edit, or analy.