K-Dense AI
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- ▌ Statistical Power · k-dense-ai bundleCalculate sample sizes, minimum detectable effects, and power curves for study planning using closed-form formulas or Monte Carlo simulation.
- ▌ Molecular Dynamics · k-dense-ai bundleRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces).
- ▌ Pathway Enrichment · k-dense-ai bundleRun pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Covers over-representation analysis (ORA), Gene Set Enrichment Analysis (GSEA), and single-sample scoring using gseapy, g:Profiler, and Enrichr libraries.
- ▌ Scholar Evaluation · k-dense-ai bundleSystematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.
- ▌ Scientific Writing · k-dense-ai bundleWrite scientific manuscripts in full paragraphs using IMRAD structure, with citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA) for research papers and journal submissions.
- ▌ Citation Management · k-dense-ai bundleSearch Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries.
- ▌ Experimental Design · k-dense-ai bundleDesign experiments and studies before data collection — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable.
- ▌ Timesfm Forecasting · k-dense-ai bundleForecast any univariate time series (sales, sensors, energy, vitals, weather) zero-shot using Google's TimesFM foundation model, with point forecasts and prediction intervals from CSV, DataFrame, or array inputs.
- ▌ Dnanexus Integration · k-dense-ai bundleBuild and deploy apps/applets on the DNAnexus cloud genomics platform, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.
- ▌ Imaging Data Commons · k-dense-ai bundleQuery and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Access large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
- ▌ Latchbio Integration · k-dense-ai bundleBuild and deploy bioinformatics workflows as serverless pipelines on the Latch platform using Python decorators, cloud data management, and GPU support.
- ▌ Neuropixels Analysis · k-dense-ai bundleAnalyze Neuropixels extracellular recordings end-to-end with SpikeInterface, covering loading, preprocessing, drift correction, spike sorting, quality metrics, and unit curation.
- ▌ Statistical Analysis · k-dense-ai bundleGuides statistical hypothesis testing with assumption checks, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting for research data.
- ▌ Benchling Integration · k-dense-ai bundleIntegrate with Benchling's Python SDK and REST API to manage registry entities, inventory, ELN entries, workflows, and Data Warehouse queries for life sciences R&D automation.
- ▌ Consciousness Council · k-dense-ai bundleSimulates a multi-perspective deliberation council to explore complex questions, decisions, or creative challenges from diverse thinking archetypes.
- ▌ Hypothesis Generation · k-dense-ai bundleFormulate testable hypotheses from observations, design experiments, and generate predictions using a structured scientific method framework.
- ▌ Opentrons Integration · k-dense-ai bundleWrite Opentrons Protocol API v2 protocols for Flex and OT-2 robots to automate liquid handling, control hardware modules, and manage labware configurations.
- ▌ Scientific Schematics · k-dense-ai bundleCreate publication-quality scientific diagrams using AI generation with smart iterative refinement and quality review.
- ▌ Labarchive Integration · k-dense-ai bundleAccess and manage LabArchives electronic lab notebooks programmatically via REST API. Create entries, upload attachments, backup notebooks, generate reports, and integrate with Protocols.io, Jupyter, REDCap, and other scientific tools.
- ▌ Get Available Resources · k-dense-ai bundleDetects available CPU, GPU, memory, and disk resources and generates strategic recommendations for scientific computing tasks.
- ▌ Iso 13485 Certification · k-dense-ai bundlePrepare ISO 13485:2016 certification documentation for medical device Quality Management Systems, including gap analysis, template-based document creation, and compliance checklists.
- ▌ Market Research Reports · k-dense-ai bundleGenerate comprehensive, professional-grade market research reports (50+ pages) with LaTeX formatting, strategic frameworks, and data-driven visualizations.
- ▌ Protocolsio Integration · k-dense-ai bundleIntegrates with the protocols.io API v3 to search, create, update, and publish scientific protocols, manage steps and materials, handle discussions, organize workspaces, and upload files.
- ▌ Markdown Mermaid Writing · k-dense-ai bundleCreates scientific documentation using markdown with embedded Mermaid diagrams as the default format, enforcing a text-based diagram standard with style guides, 24 diagram type references, and document templates.
- ▌ Scientific Brainstorming · k-dense-ai bundleGenerate novel research ideas through structured, conversational brainstorming that explores interdisciplinary connections, challenges assumptions, and identifies research gaps.
- ▌ Scientific Visualization · k-dense-ai bundleCreate publication-ready scientific figures with multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and journal-specific formatting using matplotlib, seaborn, and plotly.
- ▌ Clinical Decision Support · k-dense-ai bundleGenerate professional clinical decision support documents for pharmaceutical and clinical research, including biomarker-stratified cohort analyses and evidence-based treatment recommendation reports with GRADE grading, statistical analysis, and publication-ready LaTeX/PDF output.
- ▌ Exploratory Data Analysis · k-dense-ai bundleAutomatically detect and analyze scientific data files across 200+ formats, generating detailed markdown reports with quality metrics and analysis recommendations.
- ▌ Scientific Critical Thinking · k-dense-ai bundleEvaluate scientific claims and evidence quality by assessing experimental design, identifying biases and confounders, and applying evidence grading frameworks like GRADE and Cochrane Risk of Bias.
- ▌ Tiledbvcf · k-dense-aiStore, query, and export genomic variant data (VCF/BCF) using TileDB's sparse array technology for scalable population genomics workflows.
- ▌ Torchdrug · k-dense-ai bundleBuild and train graph neural networks for drug discovery, protein modeling, and molecular science using PyTorch-native tools.
- ▌ Etetoolkit · k-dense-ai bundleManipulate phylogenetic trees, detect evolutionary events, integrate NCBI taxonomy, and create publication-quality visualizations using the ETE toolkit.
- ▌ Exa Search · k-dense-ai bundleSearch the web and extract content from URLs using Exa, with support for academic and scientific sources.
- ▌ Markitdown · k-dense-ai bundleConvert files and office documents to Markdown using Microsoft's MarkItDown tool. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
- ▌ Matplotlib · k-dense-ai bundleCreate publication-quality static, animated, and interactive plots with fine-grained control over every element using Matplotlib's pyplot and object-oriented APIs.
- ▌ Pacsomatic · k-dense-ai bundleValidates inputs, generates samplesheets and launch scripts, and optionally executes nf-core/pacsomatic matched tumor-normal workflows from BAM files, supporting local runs and scheduler submission (LSF/Slurm/PBS/SGE).
- ▌ Paperzilla · k-dense-aiChat with your agent about projects, recommendations, and canonical papers in Paperzilla. Fetch feeds, read papers, leave feedback, and export data using the pz CLI.
- ▌ Polars Bio · k-dense-ai bundlePerform high-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames, including overlap, nearest, merge, coverage, complement, subtract, and reading/writing BED, VCF, BAM, GFF, FASTA, and FASTQ formats with streaming and cloud-native support.
- ▌ Pylabrobot · k-dense-ai bundleControl liquid handling robots, plate readers, pumps, and other lab equipment through a unified Python interface across platforms.
- ▌ Scikit Bio · k-dense-ai bundleAnalyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.
- ▌ Scvi Tools · k-dense-ai bundleProvides deep generative models for single-cell omics analysis, including probabilistic batch correction, transfer learning, differential expression, and multi-modal integration.
- ▌ Umap Learn · k-dense-ai bundlePerform nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and Parametric UMAP workflows using the umap-learn library.
- ▌ Bioservices · k-dense-ai bundleQuery 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome) with a unified Python interface for cross-database analysis, identifier mapping, and sequence analysis.
- ▌ Bulk Rnaseq · k-dense-ai bundleOrchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.
- ▌ Peer Review · k-dense-ai bundleEvaluate scientific manuscripts and grant proposals with structured, checklist-based peer review covering methodology, statistics, reproducibility, ethics, and reporting standards.
- ▌ Statsmodels · k-dense-ai bundleFit statistical models (OLS, GLM, ARIMA, mixed models) with detailed diagnostics, residuals, and inference for econometrics and time series analysis.
- ▌ Zarr Python · k-dense-ai bundleStore and process large N-dimensional arrays with chunking, compression, and parallel I/O, integrating with NumPy, Dask, and Xarray for cloud-native scientific computing.
- ▌ Infographics · k-dense-ai bundleGenerate publication-quality infographics using Nano Banana Pro AI with Gemini 3 Pro quality review and optional Perplexity Sonar research. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.
- ▌ Paper Lookup · k-dense-ai bundleSearch 10 academic literature APIs for papers, preprints, citations, and open-access full text with reproducible provenance.
- ▌ Parallel Web · k-dense-ai bundleSearch the web, extract URL content, enrich datasets with web-sourced fields, and run deep research reports, prioritizing academic and scientific sources.
- ▌ PPTX Posters · k-dense-ai bundleCreate research posters using HTML/CSS that can be exported to PDF or PPTX, with AI-generated visual elements and responsive layouts.
- ▌ Scikit Learn · k-dense-ai bundleBuild and evaluate machine learning models using scikit-learn for classification, regression, clustering, dimensionality reduction, and preprocessing.
- ▌ Transformers · k-dense-ai bundleLoad pre-trained models from Hugging Face Hub, run pipeline inference, generate text, and fine-tune models on NLP, vision, audio, and multimodal tasks using the Transformers library.
- ▌ Usfiscaldata · k-dense-ai bundleQuery the U.S. Treasury Fiscal Data REST API for federal financial data including national debt, daily and monthly treasury statements, securities auctions, interest rates, exchange rates, savings bonds, and government revenue and spending statistics. No API key required.
- ▌ Latex Posters · k-dense-ai bundleCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter with layout design, color schemes, multi-column formats, and figure integration.
- ▌ Open Notebook · k-dense-ai bundleSelf-host an open-source research notebook with AI-powered note generation, multi-speaker podcast creation, and context-aware document chat, supporting 16+ AI providers.
- ▌ Phylogenetics · k-dense-ai bundleBuild and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree, with visualization via ETE3 or FigTree for evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.
- ▌ Dhdna Profiler · k-dense-ai bundleAnalyze any text to extract a cognitive fingerprint across 12 dimensions, revealing reasoning patterns, decision styles, and thinking signatures.
- ▌ Generate Image · k-dense-ai bundleGenerate and edit high-quality images using OpenRouter's AI models including FLUX.2 Pro and Gemini 3.1 Flash Image Preview.
- ▌ What If Oracle · k-dense-ai bundleRun structured What-If scenario analysis with 4-6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use for speculative questions about uncertain futures, strategic forks, contingency planning, or stress-testing decisions.
- ▌ Database Lookup · k-dense-ai bundleQuery documented public database APIs with explicit endpoints, filters, pagination, and provenance for reproducible retrieval of scientific, regulatory, or financial facts.
- ▌ Hugging Science · k-dense-ai bundleDiscovers and uses scientific datasets, models, blog posts, and interactive demos from a curated catalog for AI/ML work in domains like biology, chemistry, physics, and genomics.
- ▌ Research Grants · k-dense-ai bundleWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC with agency-specific formatting, review criteria, budget preparation, and compliance guidance.
- ▌ Research Lookup · k-dense-ai bundleLook up current research and scientific information across three backends: fast web search, deep multi-source synthesis, and scholarly paper searches. Automatically routes each query to the best backend and saves every result for reproducible citation.
- ▌ Scikit Survival · k-dense-ai bundlePerform survival analysis and time-to-event modeling in Python using scikit-survival, including Cox models, random survival forests, gradient boosting, survival SVMs, and evaluation metrics like concordance index and Brier score.
- ▌ Torch Geometric · k-dense-ai bundleBuild and train graph neural networks with PyTorch Geometric, covering node/link/graph classification, message passing layers, heterogeneous graphs, and custom datasets.
- ▌ Treatment Plans · k-dense-ai bundleGenerate concise (3-4 page) medical treatment plans in LaTeX/PDF format across all clinical specialties, with SMART goals, evidence-based interventions, and HIPAA compliance.
- ▌ Venue Templates · k-dense-ai bundleAccess comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues, academic conferences, research posters, and grant proposals.
- ▌ Cellxgene Census · k-dense-ai bundleQuery the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data, enabling efficient access to cell metadata, gene expression slices, summary counts, and embeddings without downloading whole datasets.
- ▌ Clinical Reports · k-dense-ai bundleGenerate comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports, clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries) with templates, regulatory compliance, and validation tools.
- ▌ Ginkgo Cloud Lab · k-dense-ai bundleSubmit and manage protocols on Ginkgo Bioworks Cloud Lab for autonomous lab execution, including protein expression, purification, quantification, RNA synthesis, and custom workflows via EstiMate.
- ▌ Glycoengineering · k-dense-ai bundleAnalyze and engineer protein glycosylation by scanning sequences for N-glycosylation sequons, predicting O-glycosylation hotspots, and accessing curated glycoengineering tools for therapeutic antibody optimization and vaccine design.
- ▌ Bgpt Paper Search · k-dense-aiSearch scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions.
- ▌ Literature Review · k-dense-ai bundleConduct systematic literature reviews by searching multiple academic databases, synthesizing findings, and generating professionally formatted documents with verified citations.
- ▌ Omero Integration · k-dense-ai bundleAccess microscopy images and metadata via the OMERO Python API: retrieve datasets, analyze pixels, manage ROIs and annotations, and batch-process for high-content screening workflows.
- ▌ Pymoo · k-dense-ai bundleSolve single and multi-objective optimization problems using NSGA-II/III, MOEA/D, and other evolutionary algorithms with customizable operators, constraint handling, and benchmark problems.
- ▌ Sympy · k-dense-ai bundlePerform exact symbolic mathematics in Python — algebra, calculus, equation solving, symbolic linear algebra, and code generation via lambdify or LaTeX.
- ▌ Depmap · k-dense-ai bundleQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.
- ▌ Flowio · k-dense-ai bundleParse FCS (Flow Cytometry Standard) files v2.0-3.1, extract events as NumPy arrays, read metadata and channels, and convert to CSV or DataFrame for flow cytometry data preprocessing.
- ▌ Geniml · k-dense-ai bundleTrain unsupervised machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.
- ▌ Matlab · k-dense-ai bundlePerform numerical computing, matrix operations, data analysis, and scientific visualization using MATLAB or GNU Octave.
- ▌ Pathml · k-dense-ai bundleAnalyze whole-slide pathology images with Python: load 160+ slide formats, preprocess H&E stains, segment nuclei, construct spatial graphs, train ML models, and process multiplex immunofluorescence data (CODEX, Vectra).
- ▌ Polars · k-dense-ai bundleProcess data with high-performance DataFrames using Polars' expression-based API, lazy evaluation, and parallel execution for ETL, analytics, and pandas migration.
- ▌ Qiskit · k-dense-ai bundleBuild and execute quantum circuits on IBM Quantum hardware, simulators, and third-party providers using the Qiskit framework.
- ▌ Scanpy · k-dense-ai bundleRun standard single-cell RNA-seq analysis pipelines: QC, normalization, dimensionality reduction, clustering, differential expression, and visualization using Scanpy.
- ▌ Scvelo · k-dense-ai bundleEstimate cell state transitions from unspliced/spliced mRNA dynamics using scVelo, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data.
- ▌ Adaptyv · k-dense-ai bundleSubmit protein sequences to the Adaptyv Bio Foundry for experimental characterization (binding, thermostability, expression, fluorescence) and retrieve results via API or Python SDK.
- ▌ Anndata · k-dense-ai bundleCreate, read, manipulate, and store annotated data matrices using the AnnData Python package, designed for single-cell genomics and general-purpose annotated data workflows.
- ▌ Astropy · k-dense-ai bundlePerform astronomical data analysis with Astropy: coordinate transformations, unit conversions, FITS I/O, cosmological calculations, time handling, table operations, and WCS transformations.
- ▌ Cobrapy · k-dense-ai bundlePerform constraint-based metabolic modeling with COBRApy: run FBA, FVA, gene knockouts, flux sampling, and manage SBML models for systems biology and metabolic engineering.
- ▌ Datamol · k-dense-ai bundleSimplify molecular cheminformatics with a Pythonic wrapper around RDKit for SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, and parallel processing.
- ▌ Lamindb · k-dense-ai bundleManage biological datasets and models with LaminDB, an open-source lineage-native lakehouse. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation, collections, branches, storage, and workflow integrations.
- ▌ Matchms · k-dense-ai bundleProcess and analyze mass spectrometry data: import spectra from MGF, mzML, MSP, and JSON formats; apply 40+ filters for metadata harmonization and peak cleaning; compute spectral similarities (cosine, modified cosine) for compound identification; build reproducible processing pipelines.
- ▌ Medchem · k-dense-ai bundleApply medicinal chemistry filters for compound triage: drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and a custom query language for library filtering.
- ▌ Molfeat · k-dense-ai bundleConvert chemical structures (SMILES or RDKit molecules) into numerical representations for machine learning using 100+ featurizers, including ECFP, MACCS, descriptors, and pretrained models like ChemBERTa.
- ▌ Onekgpd · k-dense-ai bundleQuery the 1000 Genomes Project dataset at the individual participant level to find variants, carriers, and relatedness information.
- ▌ Primekg · k-dense-ai bundleQuery the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
- ▌ Pydicom · k-dense-ai bundleRead, write, and modify DICOM medical imaging files, including pixel data extraction, metadata manipulation, anonymization, and format conversion.
- ▌ Seaborn · k-dense-ai bundleCreate publication-quality statistical graphics with dataset-oriented plotting, multivariate analysis, and automatic statistical estimation using minimal code.
- ▌ Arboreto · k-dense-ai bundleInfer gene regulatory networks from gene expression data using scalable algorithms (GRNBoost2, GENIE3) with support for distributed computation.