@skills · Owner

Agent skills by k-dense-ai

165 skills indexed from github.com/k-dense-ai. Reference any of them in AdaL, Claude Code, Cursor or any coding agent — nothing to install.

• adaptyv · Skill · 32,849 stars

  How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user me

• aeon · Skill · 32,849 stars

  This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmenta

• analytical-method-validation · Skill · 32,849 stars

  Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/

• anndata · Skill · 32,849 stars

  Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the dat

• arbor · Skill · 32,849 stars

  Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis

• arboreto · Skill · 32,849 stars

  Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bul

• astropy · Skill · 32,849 stars

  Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time system

• autoskill · Skill · 32,849 stars

  Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or

• benchling-integration · Skill · 32,849 stars

  Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use whe

• bgpt-paper-search · Skill · 32,849 stars

  Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper i

• bids · Skill · 32,849 stars

  Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, micro

• biopython · Skill · 32,849 stars

  Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed acces

• bioservices · Skill · 32,849 stars

  Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with c

• bulk-rnaseq · Skill · 32,849 stars

  End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmo

• cellxgene-census · Skill · 32,849 stars

  Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell m

• cirq · Skill · 32,849 stars

  Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization expe

• citation-management · Skill · 32,849 stars

  Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citati

• clinical-decision-support · Skill · 32,849 stars

  Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artif

• clinical-reports · Skill · 32,849 stars

  Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use

• cobrapy · Skill · 32,849 stars

  Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

• consciousness-council · Skill · 32,849 stars

  Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoin

• dask · Skill · 32,849 stars

  Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. B

• database-lookup · Skill · 32,849 stars

  Query documented public database APIs with explicit endpoints, filters, pagination, and provenance. Use when a scientific, regulatory, financial, or other

• datamol · Skill · 32,849 stars

  Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardizat

• deepchem · Skill · 32,849 stars

  Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want exten

• deeptools · Skill · 32,849 stars

  NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visual

• depmap · Skill · 32,849 stars

  Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use

• dhdna-profiler · Skill · 32,849 stars

  Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive

• diffdock · Skill · 32,849 stars

  DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual

• dnanexus-integration · Skill · 32,849 stars

  Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAn

• docx · Skill · 32,849 stars

  Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include:

• esm · Skill · 32,849 stars

  Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.

• etetoolkit · Skill · 32,849 stars

  Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits an

• exa-search · Skill · 32,849 stars

  Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content.

• experimental-design · Skill · 32,849 stars

  Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are in

• exploratory-data-analysis · Skill · 32,849 stars

  Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/F

• flowio · Skill · 32,849 stars

  Read, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy ev

• fluidsim · Skill · 32,849 stars

  Plan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety ch

• generate-image · Skill · 32,849 stars

  Generate or edit images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrations, a

• geniml · Skill · 32,849 stars

  Use Geniml for audited local genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer comp

• genomic-coordinates · Skill · 32,849 stars

  Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches be

• genomic-intelligence · Skill · 32,849 stars

  Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models

• geomaster · Skill · 32,849 stars

  Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains.

• geopandas · Skill · 32,849 stars

  Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.

• get-available-resources · Skill · 32,849 stars

  Detect host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before

• gget · Skill · 32,849 stars

  Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enri

• ginkgo-cloud-lab · Skill · 32,849 stars

  Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automatio

• glycoengineering · Skill · 32,849 stars

  Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glyc

• gtars · Skill · 32,849 stars

  Use Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BED

• histolab · Skill · 32,849 stars

  Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E image

• hugging-science · Skill · 32,849 stars

  Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecolog

• hypogenic · Skill · 32,849 stars

  Plans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets. Use for the `hypogenic` package,

• hypothesis-generation · Skill · 32,849 stars

  Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, meas

• imaging-data-commons · Skill · 32,849 stars

  Query and download public cancer imaging data from NCI Imaging Data Commons. Invoke for any question about IDC collections, cancer imaging datasets, DICOM

• infographics · Skill · 32,849 stars

  Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Integrates research-lo

• iso-standards-readiness · Skill · 32,849 stars

  Prepares and structurally reviews readiness evidence for ISO management-system and laboratory-competence standards - ISO 13485 medical device QMS, ISO 1497

• labarchive-integration · Skill · 32,849 stars

  Securely integrate with the official LabArchives ELN REST-like API and Inventory API v1. Use for regional endpoint selection, signed-request construction,

• lamindb · Skill · 32,849 stars

  Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/sear

• latchbio-integration · Skill · 32,849 stars

  Build, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic

• latex-posters · Skill · 32,849 stars

  Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scie

• liteparse · Skill · 32,849 stars

  Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OC

• literature-review · Skill · 32,849 stars

  Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should

• markdown-mermaid-writing · Skill · 32,849 stars

  Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-b

• market-research-reports · Skill · 32,849 stars

  Build evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and custome

• markitdown · Skill · 32,849 stars

  Convert heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local

• matchms · Skill · 32,849 stars

  Process, clean, compare, and search tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity,

• matlab · Skill · 32,849 stars

  Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files

• matplotlib · Skill · 32,849 stars

  Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integratin

• medchem · Skill · 32,849 stars

  Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complex

• modal · Skill · 32,849 stars

  Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accele

• molecular-dynamics · Skill · 32,849 stars

  Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimizat

• molfeat · Skill · 32,849 stars

  Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecu

• networkx · Skill · 32,849 stars

  Create, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph al

• neurokit2 · Skill · 32,849 stars

  Use NeuroKit2 to build or audit reproducible research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment,

• neuropixels-analysis · Skill · 32,849 stars

  Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion corre

• nextflow · Skill · 32,849 stars

  Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.confi

• omero-integration · Skill · 32,849 stars

  Securely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering,

• onekgpd · Skill · 32,849 stars

  Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is a

• ontology-term-resolution · Skill · 32,849 stars

  Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Use whenever an ontol

• open-notebook · Skill · 32,849 stars

  Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebo

• openpiv · Skill · 32,849 stars

  Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics or flow visualiz

• opentrons-integration · Skill · 32,849 stars

  Author, review, migrate, simulate, and troubleshoot official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific li

• optimize-for-gpu · Skill · 32,849 stars

  GPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster. Use for CUDA/GPU optimization; CPU-bound NumPy, Sc

• pacsomatic · Skill · 32,849 stars

  Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate

• paper-lookup · Skill · 32,849 stars

  Search 11 academic literature APIs for papers, preprints, citations, and open-access full text, and return results with reproducible provenance. Covers Pub

• paperclip · Skill · 32,849 stars

  Search and read full-text biomedical papers, FDA/PMDA/EMA regulatory documents, clinical trial registries, and UniProt/PDB/ChEMBL entries with the Papercli

• paperzilla · Skill · 32,849 stars

  Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical

• parallel-web · Skill · 32,849 stars

  Use Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring. Best for reques

• pathml · Skill · 32,849 stars

  Use PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC pipelines, manage h5path data, quan

• pathogen-variant-surveillance · Skill · 32,849 stars

  Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing

• pathway-enrichment · Skill · 32,849 stars

  Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (diffe

• pdf · Skill · 32,849 stars

  Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multi

• peer-review · Skill · 32,849 stars

  Prepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, proto

• pennylane · Skill · 32,849 stars

  Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical

• phylogenetics · Skill · 32,849 stars

  Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or Fi

• pi-agent · Skill · 32,849 stars

  Build with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings/environment variables, creating Pi

• pkpd-modeling · Skill · 32,849 stars

  Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TM

• polars · Skill · 32,849 stars

  High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization

• polars-bio · Skill · 32,849 stars

  High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for

• pptx · Skill · 32,849 stars

  Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or pres

• pptx-posters · Skill · 32,849 stars

  Create and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Use when the requested deliver

• primekg · Skill · 32,849 stars

  Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

• protocolsio-integration · Skill · 32,849 stars

  Read, validate, and safely export protocols.io data with current official REST/MCP contracts, or create non-executing mutation plans. The bundled client ma

• pufferlib · Skill · 32,849 stars

  Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review

• pydeseq2 · Skill · 32,849 stars

  Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result vi

• pydicom · Skill · 32,849 stars

  Use pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, com

• pyhealth · Skill · 32,849 stars

  Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHR

• pylabrobot · Skill · 32,849 stars

  Develop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Use for PyLabRobot p

• pymatgen · Skill · 32,849 stars

  Analyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs, including local phase diagrams, symm

• pymc · Skill · 32,849 stars

  Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic progra

• pymoo · Skill · 32,849 stars

  Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and o

• pyopenms · Skill · 32,849 stars

  Complete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free a

• pysam · Skill · 32,849 stars

  Python/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam,

• pytdc · Skill · 32,849 stars

  Use Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access, task-aware splits, evaluator metrics, bench

• pytorch-lightning · Skill · 32,849 stars

  Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, impleme

• pyzotero · Skill · 32,849 stars

  Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and at

• qiskit · Skill · 32,849 stars

  Build, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Esti

• qutip · Skill · 32,849 stars

  Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflo

• rdkit · Skill · 32,849 stars

  Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D gene

• research-grants · Skill · 32,849 stars

  Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader im

• research-lookup · Skill · 32,849 stars

  Compile current scholarly evidence for a scientific manuscript or research brief. Use when the user explicitly asks to gather literature, references, backg

• rowan · Skill · 32,849 stars

  Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and

• scanpy · Skill · 32,849 stars

  Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression,

• scholar-evaluation · Skill · 32,849 stars

  Provide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local

• scientific-agent-skills · Collection · 32,849 stars
• scientific-brainstorming · Skill · 32,849 stars

  Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversaria

• scientific-critical-thinking · Skill · 32,849 stars

  Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grad

• scientific-schematics · Skill · 32,849 stars

  Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Only regen

• scientific-slides · Skill · 32,849 stars

  Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentati

• scientific-visualization · Skill · 32,849 stars

  Create and audit truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use for figure design, multi-panel layouts

• scientific-writing · Skill · 32,849 stars

  Draft, revise, and audit scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, conf

• scikit-bio · Skill · 32,849 stars

  Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Ne

• scikit-learn · Skill · 32,849 stars

  Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, di

• scikit-survival · Skill · 32,849 stars

  Build, evaluate, and audit right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection,

• scvelo · Skill · 32,849 stars

  RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time,

• scvi-tools · Skill · 32,849 stars

  Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with unce

• seaborn · Skill · 32,849 stars

  Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive d

• shap · Skill · 32,849 stars

  Explain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, han

• simpy · Skill · 32,849 stars

  Build, inspect, test, and analyze bounded process-based discrete-event simulations with SimPy, including events, resources, interrupts, monitoring, replica

• skills · Collection · 32,849 stars
• stable-baselines3 · Skill · 32,849 stars

  Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick proto

• statistical-analysis · Skill · 32,849 stars

  Guided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted

• statistical-power · Skill · 32,849 stars

  Sample-size and statistical power calculations for planning studies. Use whenever someone asks "how many subjects/samples/replicates do I need", wants an a

• statsmodels · Skill · 32,849 stars

  Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and i

• sympy · Skill · 32,849 stars

  Use when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX. Pref

• tamarind · Skill · 32,849 stars

  Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GP

• tiledbvcf · Skill · 32,849 stars

  Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel

• timesfm-forecasting · Skill · 32,849 stars

  Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) with

• torch-geometric · Skill · 32,849 stars

  PyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neigh

• torchdrug · Skill · 32,849 stars

  Build and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesi

• transformers · Skill · 32,849 stars

  Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimoda

• treatment-plans · Skill · 32,849 stars

  Format and structurally validate local treatment-plan documentation after clinical decisions have already been supplied and verified by authorized licensed

• umap-learn · Skill · 32,849 stars

  Use UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP

• uncertainty-and-units · Skill · 32,849 stars

  Track physical units and propagate measurement uncertainty in scientific calculations using pint and uncertainties. Use for unit conversion and dimensional

• usfiscaldata · Skill · 32,849 stars

  Query 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 Sta

• vaex · Skill · 32,849 stars

  Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame opera

• venue-templates · Skill · 32,849 stars

  Prepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX scaffolds.

• what-if-oracle · Skill · 32,849 stars

  Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use when the u

• xlsx · Skill · 32,849 stars

  Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting

• zarr-python · Skill · 32,849 stars

  Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/Xarray compatible, for large-scale sci

• deepspot-m · Skill

  Generate transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Use when you need spatial gene expression in log1p-CPM for

• lab-hardware-cad · Skill

  Design custom laboratory hardware as parametric build123d models and export fabrication-ready STEP, STL, and DXF files - microfluidic chips and molds, opto

• ncats-arax · Skill

  Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relatio

• relsa-severity-assessment · Skill

  Multivariate severity assessment and humane endpoint prediction for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIM

• waypoint-bio · Skill

  Use when working with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pret

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