Validate Illumina BCL run folders and sample sheets, plan demultiplexing—the separation of reads by sample—and convert data to FASTQ using installed tools. Review conversion metrics, index settings, and reads that could not be assigned.
Find the right workflow for next-generation sequencing data by inspecting files and clarifying only missing setup details. Receive a recommended analysis skill, checks of available tools, and plans for software installation and reference data.
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.
Retrieve focused genome, assembly, and taxonomy metadata from NCBI Datasets v2, a biological data service. Get concise Markdown summaries by default, with raw JSON or text available when requested.
Prepare single-cell or single-nucleus RNA-seq analysis by checking inputs and selecting workflows that turn FASTQ sequencing files into count matrices. Route quality checks, cell annotation, clustering, and UMAP visualization to the embedded downstream skill.
Plan or run bulk RNA-seq analysis to find genes whose expression differs between conditions. Check sample replication, study design, batch effects, and data quality, then produce comparison tables, diagnostic plots, and ranked gene lists.
Set up and operate NVIDIA AI-Q Blueprint locally or on your own infrastructure. Choose a deployment mode, configure credentials, check service health, troubleshoot failures, and provide a verified server address for aiq-research.
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.
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.
Turn Notion product requirements and feature specifications into linked implementation plans and manageable tasks. Extract requirements, flag ambiguities, and keep task status, milestones, blockers, and decisions aligned as work progresses.
Routes bulk RNA-seq requests to workflows for generating expression counts and checking quality, or comparing gene expression between groups. Checks input data, sample information, and analysis requirements before directing the next step.
Plan or run targeted DNA panel analysis using UMIs, barcodes that identify DNA molecules. Organize consensus reads, coverage checks, and low-frequency variant results with molecular support, filtering reasons, and explicit quality limitations.
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.
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.
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.
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.
Plan or run DNA analysis to find small genetic changes in tumors, using tumor samples alone or paired with normal tissue. Check sample pairing, contamination, data quality, filtering, and annotations that add information to detected variants.
Retrieve concise summaries from Reactome about biological pathways, events, participating molecules, and diagram-related data. Look up specific identifiers, search for relevant entries, or find pathways associated with an entity, and save the full response when needed.
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.
Turn broad life sciences questions into focused research plans. Resolve names and identifiers for genes, diseases, or compounds, select relevant research skills, and combine evidence into a concise answer that explains uncertainty and useful follow-up analyses.
Plan or run bulk RNA-seq processing from sequencing reads to count matrices, tables of expression counts across samples. Check sample metadata, reference consistency, read mapping, and quantification quality, and produce summaries for downstream analysis.
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.
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.
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.
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