12,203 skills found · Page 30 of 407
K-Dense-AI / arborApplies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis and benchmark optimization.
K-Dense-AI / astropyCore 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 / bulk-rnaseqPrepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff.
K-Dense-AI / clinical-reportsCreates safety-bounded draft structures and runs local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.
K-Dense-AI / cobrapyPerforms constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for systems biology and metabolic engineering.
K-Dense-AI / daskScales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask. Covers DataFrames, Arrays, Bags, Futures, chunking, schedulers, and distributed diagnostics.
K-Dense-AI / dataladRetrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and containers-run
K-Dense-AI / deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
K-Dense-AI / diffdockPredicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triage, confidence interpretation, and validation. Use for molecular docking and virtual-screening pose generation, not binding-affinity prediction.
K-Dense-AI / esmUses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and Biohub hosted clients, including former Forge workflows; distinguishes the separate legacy fair-esm distribution.
K-Dense-AI / experimental-designDesigns experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable
K-Dense-AI / exploratory-data-analysisPerforms bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffold…
K-Dense-AI / fluidsimPlans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks. Use for FluidSim solver selection, parameter review, FFT/MPI setup, output diagnostics, or restart compatibility.
K-Dense-AI / genimlSupports 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 / genomic-intelligenceOptional gi_ bearer key for the REST /v1 API and higher MCP rate and concurrency limits. The hosted MCP demo runs keyless; request a key at contact@genomicintelligence.ai.
K-Dense-AI / geomasterSupports geospatial research workflows for remote sensing, vector and raster GIS, spatial statistics, terrain and network analysis, and machine learning for Earth observation
K-Dense-AI / glycoengineeringAnalyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evidence, and preparing NetNGlyc, NetOGlyc and GlycoSHIELD workflows.
K-Dense-AI / gtarsSupports 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 the CLI.
K-Dense-AI / hypogenicPlans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets. Use for the `hypogenic` package, its task configs, hypothesis banks, or HypoBench datasets—not for manual hypothesis formulation or scientific validation.
K-Dense-AI / imaging-data-commonsQueries and downloads public cancer imaging data from NCI Imaging Data Commons. Supports IDC collection discovery, DICOM access, radiology (CT, MR, PET) and pathology AI datasets, metadata SQL, visualization, licensing, and citations.
K-Dense-AI / iso-standards-readinessPrepares and structurally reviews readiness evidence for ISO management-system and laboratory-competence standards - ISO 13485 medical device QMS, ISO 14971 device risk management, ISO/IEC 17025 testing and calibration laboratories, and ISO 15189 medical laboratories
K-Dense-AI / lab-hardware-cadDesigns 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 adapters, cuvette and microplate holders, tube racks, animal-behavior rigs, and 3D-printed instrument f…
K-Dense-AI / lamindbManages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage, and workflow integrations. Use for reproducible biological data curation or a LaminDB lakehouse.
K-Dense-AI / markdown-mermaid-writingWrites scientific Markdown documentation and Mermaid diagrams for workflows, relationships, timelines, and schemas. Provides syntax references, document templates, accessibility guidance, and version-aware rendering checks
K-Dense-AI / market-research-reportsBuilds evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, competitive landscapes, TAM/SAM/SOM reconciliation, forecast sensitivity, and auditable report scaffolds.
K-Dense-AI / matplotlibCreates and customizes scientific plots with Matplotlib. Used for fine-grained control over plot elements, novel plot types, and scientific workflows. Export to PNG/PDF/SVG for publication.
K-Dense-AI / molecular-dynamicsRuns and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces).
K-Dense-AI / molfeatFeaturizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints, RDKit descriptors, pharmacophores, pretrained embeddings, configuration persistence, and molecule-to-label alignment.
K-Dense-AI / neurokit2Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability, and complexity
K-Dense-AI / nextflowBuilds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files, nextflow.config, processes/channels/operators, samplesheets, nf-test, modules/subworkflows, container and executor configuration, HPC/SLURM or cloud deployment, and failed or resumed pipelin…
