Research & Science · By K-Dense-AI

Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research.

K-Dense-AI/scientific-agent-skills

Processes, cleans, compares, and searches tandem mass spectra with matchms.

K-Dense-AI/scientific-agent-skills

Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships.

K-Dense-AI/scientific-agent-skills

Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs.

K-Dense-AI/scientific-agent-skills

Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4).

K-Dense-AI/scientific-agent-skills

Performs Particle Image Velocimetry (PIV) analysis with OpenPIV.

K-Dense-AI/scientific-agent-skills

Authors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots.

K-Dense-AI/scientific-agent-skills

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs.

K-Dense-AI/scientific-agent-skills

Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex quantification, spatial graphs, and bounded model inference.

K-Dense-AI/scientific-agent-skills

Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies.

K-Dense-AI/scientific-agent-skills

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results.

K-Dense-AI/scientific-agent-skills

Queries a pinned Precision Medicine Knowledge Graph (PrimeKG) CSV for typed gene, drug, disease, and phenotype nodes, direct associations, disease context, and one- or two-hop paths.

K-Dense-AI/scientific-agent-skills

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage…

K-Dense-AI/scientific-agent-skills

Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen.

K-Dense-AI/scientific-agent-skills

Provides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits, evaluator metrics, benchmark groups, and bounded molecular-oracle scoring.

K-Dense-AI/scientific-agent-skills

Builds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime.

K-Dense-AI/scientific-agent-skills

Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows.

K-Dense-AI/scientific-agent-skills

Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts.

K-Dense-AI/scientific-agent-skills

A skill your agent uses when starting analysis work that needs isolation, or before executing a pre-registered plan - ensures an isolated, reproducible workspace with pinned environment, fixed…

K-Dense-AI/science-superpowers

Designs custom laboratory hardware as parametric build123d models and exports fabrication artifacts as STEP, STL, and DXF files - microfluidic chips and molds, optomechanical mounts and breadboard…

K-Dense-AI/scientific-agent-skills

Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants.

K-Dense-AI/scientific-agent-skills

Applies the computational biology and AI-driven reasoning of Aviv Regev (computational biologist, Genentech, single-cell genomics).

K-Dense-AI/mimeographs

Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements.

K-Dense-AI/scientific-agent-skills

Reads, validates, and safely exports protocols.io data with current official REST/MCP contracts, or creates non-executing mutation plans.

K-Dense-AI/scientific-agent-skills

Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes.

K-Dense-AI/scientific-agent-skills

Develops and reviews PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations.

K-Dense-AI/scientific-agent-skills

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or…

K-Dense-AI/scientific-agent-skills

Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties.

K-Dense-AI/scientific-agent-skills

Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts.

K-Dense-AI/scientific-agent-skills

Supports research proposal preparation and review for NSF, NIH, DOE, DARPA, and Taiwan NSTC, including opportunity-specific requirements, aims, review criteria, budgets, broader impacts, forms, and…

K-Dense-AI/scientific-agent-skills

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology.

K-Dense-AI/scientific-agent-skills

Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis and benchmark optimization.

K-Dense-AI/scientific-agent-skills

Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets.

K-Dense-AI/scientific-agent-skills

Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem.

K-Dense-AI/scientific-agent-skills

Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data.

K-Dense-AI/scientific-agent-skills

Structures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges.

K-Dense-AI/scientific-agent-skills

Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and containers-run.

K-Dense-AI/scientific-agent-skills

Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained…

K-Dense-AI/scientific-agent-skills

Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers, and PRISM drug sensitivity.

K-Dense-AI/scientific-agent-skills

Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow.

K-Dense-AI/scientific-agent-skills

Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4.

K-Dense-AI/scientific-agent-skills

Searches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches.

K-Dense-AI/scientific-agent-skills

Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibility, and assess consensus universes.

K-Dense-AI/scientific-agent-skills

Detects host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly resource-sensitive local workload.

K-Dense-AI/scientific-agent-skills

Queries 20+ bioinformatics resources through CLI/Python. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and…

K-Dense-AI/scientific-agent-skills

Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog.

K-Dense-AI/scientific-agent-skills

Integrates with the official LabArchives ELN REST-like API and Inventory API v1.

K-Dense-AI/scientific-agent-skills