Look up Gene Ontology terms, which classify gene functions, and their links to gene products through QuickGO. Get concise summaries, explore broader or narrower terms, and save full responses when needed.
Plan DNA variant detection workflows by identifying the assay and sample model, then routing to germline, cancer somatic, or molecular-barcode panel skills. It also supports focused local BAM/CRAM checks with variant files, depth summaries, and optional filters.
Analyze marker-gene sequencing data to study microbial communities. Supports FASTQ quality checks and, with primers, metadata, and taxonomy resources, workflows that produce sequence variant tables, taxonomic assignments, diversity measurements, and plots.
Build or review quality control workflows for single-cell and single-nucleus RNA sequencing data. Select filters from observed data, detect doublets, assign cell types, and create UMAP plots that summarize cell relationships, while recording analysis decisions and outputs.
Manage Mixpanel Headless login and connection settings, check credentials, and switch accounts, projects, or workspaces. Save named combinations of these settings as targets so an agent can select the intended connection together.
Find and inspect UI components in MagicPath, add them to an app, and adapt their behavior and styling. Apply themes or create and edit canvas components from code, including work based on an existing repository interface.
Look up one genetic variant in UKB-TOPMed and summarize its associations with traits. Accept rsID identifiers or GRCh37 and GRCh38 coordinates, resolve the required query format, and report association totals and any result truncation.
Query STRING for protein interaction networks, interaction partners, and enrichment results showing functions common in a gene set. Receive concise summaries with limited result counts, with options for machine-readable JSON or saved full results.
Retrieve focused information from PubChem, including molecular formulas, molecular weights, compound descriptions, assay summaries, and substance metadata. Get concise Markdown summaries, with the option to save the full response for further use.
Plan or run quality checks and peak calling, which identifies enriched genomic regions, for ChIP-seq, CUT&RUN, and CUT&Tag. The workflow accounts for controls and replicates and prepares signal tracks, quality reports, and differential binding designs.
Plan or run ATAC-seq analysis to identify accessible DNA regions. Check sequencing quality, align reads, detect peaks, combine evidence across replicate samples, and prepare comparisons between conditions with quality summaries and visualization tracks.
Validate FASTQ sequencing files, run local quality checks, and interpret reports to decide whether trimming is needed. Optionally remove adapters or low-quality read ends while preserving original reads and their quality reports.
Retrieve genes, genetic variants, clinical annotations, and dosing guidelines from the PharmGKB API, then turn the results into concise summaries. Save the full response when you need the underlying data.
Organize ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag inputs and route them to suitable analysis workflows. Covers initial quality checks and preparation for finding peaks, genomic regions with concentrated signal, and comparing them across samples.
Find proteomics projects, which study proteins on a broad scale, in PRIDE Archive and summarize their metadata. Search by keyword or use a PXD accession to inspect a specific project's registered information.
Prepare a Python environment for Mixpanel analysis by installing required libraries and checking credentials and connectivity. Use it for first-time setup, missing dependencies, or guidance on service account and OAuth sign-in options.
Look up TPMI associations for a single genetic variant using an rsID or genome coordinates. Get a concise summary showing the queried variant, the total number of associations, and whether the displayed results are incomplete.
Guide the use of NVIDIA cuOpt for route planning and mathematical optimization, choosing values to minimize cost or maximize profit under constraints. Covers requirements, environment checks, installation guidance, and verification of solver results.
Look up RNA entries in RNAcentral by identifier or targeted search, retrieve cross-references to related database records, and receive concise summaries. Raw JSON output is also available when requested for further processing.
Search Rhea, a biochemical reaction database, using reaction IDs, compound names, enzyme classification numbers, or reaction terms. Get concise summaries of focused search results, with raw JSON available when you need machine-readable output.
Analyze Mixpanel data with Python to explore usage trends, conversion steps, returning users, and differences between user groups. Also manage business context documents that explain an organization's structure and goals to AI assistants.
Prepare meeting agendas and reading materials using relevant Notion pages and supplemental research. Tailor the content to attendees and required decisions, with source links, discussion owners, time allocations, and follow-up actions.
Retrieve focused target, disease, drug, variant, and study data from Open Targets Platform. Produce concise summaries or disease-by-source evidence matrices to compare available evidence while keeping queries and returned results compact.
Start shotgun metagenomics workflows for mixed-community DNA reads in FASTQ files. Check read quality, remove host sequences, and profile organisms and biological functions using supported tools and databases, producing tables and visual summaries when results are available.
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