K-Dense-AI
Showing 61–120 of 159 skills · Page 2 of 3
K-Dense-AI / opentrons-integration
46.4kAuthor, review, migrate, simulate, and troubleshoot 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 / optimize-for-gpu
46.4kGPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster. Use for CUDA/GPU optimization; CPU-bound NumPy, SciPy, pandas, scikit-learn, NetworkX, scikit-image, vector-search, image-processing, graph, simulation, or file-I/O workloads; CuPy, cuDF, cuML, c…
K-Dense-AI / pacsomatic
46.4kOperator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and…
K-Dense-AI / paper-lookup
46.4kSearch 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and return results with reproducible provenance.
K-Dense-AI / paperclip
46.4kPaperclip API key from https://paperclip.gxl.ai/keys. Preferred over browser OAuth. Not required — the skill also covers installing the CLI and signing in interactively.
K-Dense-AI / pathml
46.4kUse PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC pipelines, manage h5path data, quantify multiplex images, construct spatial graphs, and plan bounded model inference.
K-Dense-AI / pathogen-variant-surveillance
46.4kQuery live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry
K-Dense-AI / peer-review
46.4kPrepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, protocols, preprints, or research proposals; reporting-guideline selection; claim–evidence checks; methods, statistics, reproducibility, ethics, figur…
K-Dense-AI / phylogenetics
46.4kBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
K-Dense-AI / pi-agent
46.4kBuild with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings/environment variables, creating Pi skills/extensions/packages/themes/prompt templates, embedding Pi through the SDK, integrating over RPC or JSON event streams, parsing sessions,…
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
46.4kHigh-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-core processing, Arrow interoperability, and optional GPU execution.
K-Dense-AI / polars-bio
46.4kHigh-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.
K-Dense-AI / pptx-posters
46.4kCreate and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets
K-Dense-AI / primekg
46.4kQuery the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
K-Dense-AI / pufferlib
46.4kVersion-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review
K-Dense-AI / pydeseq2
46.4kDifferential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.
K-Dense-AI / pydicom
46.4kUse pydicom to read, inspect, write, transform, and safely preflight 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 / pyhealth
46.4kBuild clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models…
K-Dense-AI / pylabrobot
46.4kDevelop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Use for PyLabRobot protocols or API questions; keep physical execution behind an explicit operator safety gate.
K-Dense-AI / pymatgen
46.4kAnalyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs, including local phase diagrams, symmetry sensitivity, electronic-structure I/O, and explicitly bounded Materials Project queries.
K-Dense-AI / pymc
46.4kBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
K-Dense-AI / pymoo
46.4kMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
K-Dense-AI / pyopenms
46.4kComplete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free and isobaric quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms.
K-Dense-AI / pytdc
46.4kUse Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access, task-aware splits, evaluator metrics, benchmark groups, and bounded molecular-oracle workflows.
K-Dense-AI / pytorch-lightning
46.4kDeep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network traini…
K-Dense-AI / qiskit
46.4kBuild, simulate, transpile, and execute 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, and Qi…
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 / rdkit
46.4kCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit).
K-Dense-AI / relsa-severity-assessment
46.4kMultivariate severity assessment and humane endpoint prediction for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast forecasting
K-Dense-AI / research-grants
46.4kWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
K-Dense-AI / scanpy
46.4kStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy.
K-Dense-AI / scholar-evaluation
46.4kProvide 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 / 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-critical-thinking
46.4kEvaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws.
K-Dense-AI / scientific-visualization
46.4kCreate and audit truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use 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
46.4kDraft, revise, and audit 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
46.4kBuild, evaluate, and audit 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 / scvelo
46.4kRNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
K-Dense-AI / seaborn
46.4kStatistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib.
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.
K-Dense-AI / simpy
46.4kBuild, inspect, test, and analyze bounded process-based discrete-event simulations with SimPy, including events, resources, interrupts, monitoring, replications, warm-up, and reproducible output analysis.
K-Dense-AI / stable-baselines3
46.4kProduction-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments.
K-Dense-AI / statistical-analysis
46.4kGuided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting
K-Dense-AI / sympy
46.4kUse when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX. Prefer NumPy or SciPy when floating-point approximations are sufficient.
K-Dense-AI / tiledbvcf
46.4kEfficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.
K-Dense-AI / timesfm-forecasting
46.4kZero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals.
K-Dense-AI / torch-geometric
46.4kPyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets
K-Dense-AI / torchdrug
46.4kBuild and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and knowledge graph reasoning
K-Dense-AI / transformers
46.4kHugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tasks
K-Dense-AI / treatment-plans
46.4kFormat and structurally validate local treatment-plan documentation after clinical decisions have already been supplied and verified by authorized licensed professionals.
K-Dense-AI / umap-learn
46.4kUse UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and Parametric UMAP workflows.
K-Dense-AI / uncertainty-and-units
46.4kTrack physical units and propagate measurement uncertainty in scientific calculations using pint and uncertainties. Use for unit conversion and dimensional checking, GUM uncertainty budgets, Type A and Type B evaluation, coverage factors and expanded uncertainty, Monte Carlo propagation, significant…
K-Dense-AI / usfiscaldata
46.4kQuery the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates, foreign exchange rates, savings bonds, or U.S.
K-Dense-AI / vaex
46.4kUse this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets.
K-Dense-AI / venue-templates
46.4kPrepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX scaffolds
K-Dense-AI / waypoint-bio
46.4kHugging Face read token with access to the gated outpost-bio/Waypoint-*, outpost-bio/Atlas, and outpost-bio/Compass repos.
K-Dense-AI / what-if-oracle
46.4kRun structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order)
K-Dense-AI / xlsx
46.4kCreate, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel.