dralkh/seerai
58 skills
$npx skills add dralkh/seeraiSkillInstalls
adaptyvHow to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval.aeonThis skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection,…anndataData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem.arborAutonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree…arboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).astropyCore Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems,…autoskillObserve the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or…benchling-integrationBenchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries.bgpt-paper-searchSearch scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.bidsUse this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET,…biopythonComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access…bioservicesUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with…bulk-rnaseqEnd-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon,…cellxgene-censusQuery the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data.cirqGoogle quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization…citation-managementComprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and…clinical-decision-supportGenerate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses…clinical-reportsWrite comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3,…cobrapyConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.consciousness-councilRun a multi-perspective Mind Council deliberation on any question, decision, or creative challenge.daskDistributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters.database-lookupDeterministically query 78 public scientific, biomedical, materials science, regulatory, finance, and demographics databases through documented REST APIs.datamolPythonic wrapper around RDKit with simplified interface and sensible defaults.deepchemMolecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive…deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq…depmapQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles.dhdna-profilerExtract cognitive patterns and thinking fingerprints from any text.diffdockDiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual…dnanexus-integrationDNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline…docxUse this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files).esmUse when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.etetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for…exa-searchWeb toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content.experimental-designDesign experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so the results will…exploratory-data-analysisPerform comprehensive exploratory data analysis on scientific data files across 200+ file formats.flowioParse 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…fluidsimFramework for computational fluid dynamics simulations using Python.generate-imageGenerate or edit images using AI models (FLUX, Nano Banana 2).genimlThis skill should be used when working with genomic interval data (BED files) for machine learning tasks.geomasterComprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains.geopandasPython library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files.get-available-resourcesThis skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs,…ggetFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures,…ginkgo-cloud-labSubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation…glycoengineeringAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated…gtarsHigh-performance toolkit for genomic interval analysis in Rust with Python bindings.histolabLightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images.hugging-scienceUse when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology,…hypogenicAutomated LLM-driven hypothesis generation and testing on tabular datasets.hypothesis-generationStructured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with…imaging-data-commonsQuery and download public cancer imaging data from NCI Imaging Data Commons using idc-index.infographicsCreate professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review.iso-13485-certificationComprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems.labarchive-integrationElectronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for…lamindbUse when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models.latchbio-integrationLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir,…latex-postersCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter.liteparseLocal document and PDF parsing with spatial text and bounding boxes.