K-Dense-AI
Showing 1–60 of 174 skills · Page 1 of 3
K-Dense-AI / aeon
46.4kThis skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search
K-Dense-AI / alphagenome
46.4kAlphaGenome API key, free for non-commercial use from deepmind.google.com/science/alphagenome. ALPHA_GENOME_API_KEY is accepted as an alternative spelling.
K-Dense-AI / analytical-method-validation
46.4kPlans, executes, and documents validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025.
K-Dense-AI / anndata
46.4kHandles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
K-Dense-AI / arbor
46.4kApplies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis and benchmark optimization.
K-Dense-AI / astropy
46.4kCore 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-rnaseq
46.4kPrepares 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-reports
46.4kCreates 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 / cobrapy
46.4kPerforms 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 / dask
46.4kScales 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 / datalad
46.4kRetrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and containers-run
K-Dense-AI / deeptools
46.4kNGS 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 / diffdock
46.4kPredicts 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 / esm
46.4kUses 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-design
46.4kDesigns 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-analysis
46.4kPerforms 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 / fluidsim
46.4kPlans, 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 / geniml
46.4kSupports 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-intelligence
46.4kOptional 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 / geomaster
46.4kSupports 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 / glycoengineering
46.4kAnalyzes 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 / gtars
46.4kSupports 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 / hypogenic
46.4kPlans 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-commons
46.4kQueries 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-readiness
46.4kPrepares 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-cad
46.4kDesigns 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 / lamindb
46.4kManages 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-writing
46.4kWrites 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-reports
46.4kBuilds 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 / matplotlib
46.4kCreates 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-dynamics
46.4kRuns 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 / molfeat
46.4kFeaturizes 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 / neurokit2
46.4kBuilds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability, and complexity
K-Dense-AI / nextflow
46.4kBuilds, 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…
K-Dense-AI / onekgpd
46.4kQueries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants
K-Dense-AI / opentrons-integration
46.4kAuthors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific liquid handling, deck and labware setup, pipettes, modules, runtime parameters, liquid classes, and Opentrons App analysis.
K-Dense-AI / paper-lookup
46.4kSearches 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and returns results with reproducible provenance.
K-Dense-AI / paperclip
46.4kPaperclip API key from https://paperclip.gxl.ai/keys. Existing OAuth credentials also work; installation and help do not require a key.
K-Dense-AI / pathogen-variant-surveillance
46.4kQueries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies.
K-Dense-AI / pathway-enrichment
46.4kPerforms pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pa…
K-Dense-AI / peer-review
46.4kPrepares evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Supports authorized review of scientific manuscripts, protocols, preprints, or research proposals; reporting-guideline selection; claim–evidence checks; methods, statistics, reproducibility, ethics, fig…
K-Dense-AI / phylogenetics
46.4kBuilds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization.
K-Dense-AI / pkpd-modeling
46.4kPharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug moni…
K-Dense-AI / polars-bio
46.4kPerforms genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data.
K-Dense-AI / primer-design
46.4kDesigns and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates.
K-Dense-AI / pufferlib
46.4kVersion-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review. Covers the native 5.0 build and environment API, published 3.0.0 Gymnasium/PettingZoo adaptation, and a pinned historical 4.0 profile.
K-Dense-AI / pydeseq2
46.4kPerforms bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.
K-Dense-AI / pydicom
46.4kReads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugins, frames, private elements, JSON, and bounded de-identification review.
K-Dense-AI / pymatgen
46.4kAnalyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry sensitivity, electronic-structure I/O, and bounded Materials Project queries.
K-Dense-AI / pysam
46.4kProvides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
K-Dense-AI / pytdc
46.4kProvides 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 / qutip
46.4kSimulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for local quantum-dynamics work where physical assumptions, dimensions, and numerical convergence must be explicit.
K-Dense-AI / relsa-severity-assessment
46.4kSupports multivariate severity assessment and exploratory endpoint-time score forecasting for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast forecasting
K-Dense-AI / scanpy
46.4kPerforms Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad.
K-Dense-AI / scientific-brainstorming
46.4kFacilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs.
K-Dense-AI / scientific-visualization
46.4kCreates and audits truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use it for figure design, multi-panel layouts, uncertainty and missing-data displays, color/contrast review, image metadata validation, and journal export planning.
K-Dense-AI / scientific-writing
46.4kDrafts, revises, and audits scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistency checks.
K-Dense-AI / scikit-bio
46.4kBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
K-Dense-AI / scikit-survival
46.4kBuilds, evaluates, and audits right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection, probability prediction, and censoring-aware metrics.
K-Dense-AI / shap
46.4kExplain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, handling multi-output explanations, and producing local or global SHAP visualizations.