14,567 skills found · Page 35 of 486
K-Dense-AI / datamolPythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects.
K-Dense-AI / deepchemBuilds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained encoder transfer.
K-Dense-AI / deepspot-mGenerates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from 224x224 tiles at about 20x, querying the released protein-coding gene panel by symbol, and whole-slide prediction after resolution-aware tiling with histolab.
K-Dense-AI / depmapRetrieves 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 / dnanexus-integrationBuilds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Supports DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.
K-Dense-AI / etetoolkitAnalyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploratio…
K-Dense-AI / flowioReads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy event extraction, multi-dataset files, table export, and FCS 3.1 creation; use FlowKit for compensation, cytometry transforms, gating, or FlowJo…
K-Dense-AI / flowkitAnalyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strategies, and supported FlowJo 10 workspaces.
K-Dense-AI / folklore-variant-evidenceRetrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple indel through Folklore Clinical Variant Interpretation MCP.
K-Dense-AI / genomic-coordinatesConverts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis.
K-Dense-AI / geopandasGuidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.
K-Dense-AI / get-available-resourcesDetects 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 / latchbio-integrationBuilds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP
K-Dense-AI / liteparseLocal document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON for RAG; batch-ingesting folders of papers; or rendering pages to PNG for multimodal agents.
K-Dense-AI / markitdownConverts heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local conversion, streams, Office/PDF/data formats, batch workflows, plugins, vision OCR, Azure extraction, and the official MCP server.
K-Dense-AI / matchmsProcesses, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks.
K-Dense-AI / matlabBuilds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows. Use for arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.
K-Dense-AI / medchemApplies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.
K-Dense-AI / ncats-araxQueries 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 / ontology-term-resolutionResolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry, resolves compact identifiers via Identifiers.org, maps lab shorthand with ZOOMA, and builds Ontobee term pages
K-Dense-AI / pathmlSupports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex quantification, spatial graphs, and bounded model inference. Use for whole-slide H&E, CODEX, Vectra, Mesmer, HoVer-Net, and HACTNet workflows.
K-Dense-AI / pennylaneBuilds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows. Use for variational quantum algorithms, quantum machine learning, simulator validation, and moving validated circuits to provider plugins.
K-Dense-AI / polarsHigh-performance DataFrame library for Python ETL, analytics, and pandas migration. It supports expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-core processing, Arrow interoperability, and optional GPU execution.
K-Dense-AI / pptx-postersCreates and audits editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets.
K-Dense-AI / pymcBuilds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference, mutable-data predictions, posterior predictive checks, diagnostics, and PSIS-LOO model comparison. Use for probabilistic modeling and uncertainty inference in PyMC.
K-Dense-AI / pymooSolves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D, constraints, Pareto approximations, reference directions, and ZDT/DTLZ benchmarks for engineering and research problems.
K-Dense-AI / pyopenmsProcesses mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms.
K-Dense-AI / qiskitBuilds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches, error mitigation, an…
K-Dense-AI / scholar-evaluationProvides qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality controls. Never use for ranking people or consequential decisions.
K-Dense-AI / scikit-learnSupports machine learning in Python with scikit-learn. Applies when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines.
