← all plugins

1. ▌
   esm · lingxling bundle

   Generates and analyzes protein sequences and structures using ESM3, ESMC, and ESMFold2, with support for local and cloud inference.
   253
   repo stars
2. ▌
   aeon · lingxling bundle

   Runs time series machine learning tasks—classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search—using the scikit-learn compatible aeon toolkit.
   253
   repo stars
3. ▌
   bids · lingxling bundle

   Organize, query, validate, and convert neuroscience datasets following the Brain Imaging Data Structure (BIDS) standard, including metadata sidecars and derivatives.
   253
   repo stars
4. ▌
   cirq · lingxling bundle

   Design, simulate, and run quantum circuits on Google Quantum AI and partner hardware using Cirq, including noise modeling and characterization experiments.
   253
   repo stars
5. ▌
   dask · lingxling bundle

   Scales pandas and NumPy workflows to datasets larger than memory using parallel and distributed computing, with support for dataframes, arrays, bags, and custom task graphs.
   253
   repo stars
6. ▌
   gget · lingxling bundle

   Queries 20+ bioinformatics databases from the command line or Python for gene info, sequences, BLAST/BLAT, protein structures, viral data, and expression metrics.
   253
   repo stars
7. ▌
   pymc · lingxling bundle

   Build, fit, validate, and compare Bayesian models using PyMC, including hierarchical models, MCMC sampling, variational inference, posterior predictive checks, and model comparison.
   253
   repo stars
8. ▌
   shap · lingxling bundle

   Explains machine learning model predictions using SHAP values, covering feature importance, visualizations, debugging, bias analysis, and production deployment.
   253
   repo stars
9. ▌
   vaex · lingxling bundle

   Process and analyze tabular datasets larger than RAM using lazy, out-of-core DataFrames, with fast aggregations, visualization, and machine learning integration.
   253
   repo stars
10. ▌
    arbor · lingxling bundle

    Runs an autonomous optimization loop that iteratively improves an artifact against an objective and evaluator using Hypothesis Tree Refinement, with subagent executors in isolated git worktrees.
    253
    repo stars
11. ▌
    gtars · lingxling bundle

    High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
    253
    repo stars
12. ▌
    modal · lingxling bundle

    Deploy and scale Python AI/ML workloads on Modal's serverless cloud, including GPU compute, web endpoints, scheduled jobs, and persistent storage.
    253
    repo stars
13. ▌
    pymoo · lingxling bundle

    Solves single- and multi-objective optimization problems with NSGA-II/III, MOEA/D, and other evolutionary algorithms, including constraint handling, Pareto front analysis, and benchmark problems.
    253
    repo stars
14. ▌
    pysam · lingxling bundle

    Read, write, and analyze genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.
    253
    repo stars
15. ▌
    pytdc · lingxling bundle

    Access AI-ready drug discovery datasets, benchmarks, and molecular oracles from Therapeutics Data Commons for therapeutic machine learning and pharmacological prediction.
    253
    repo stars
16. ▌
    qutip · lingxling bundle

    Simulate and analyze quantum mechanical systems, including open quantum systems, using QuTiP's solvers for master equations, Lindblad dynamics, and quantum trajectories.
    253
    repo stars
17. ▌
    rdkit · lingxling bundle

    Provides guidance for using RDKit to read and write molecular structures, calculate descriptors, generate fingerprints, perform substructure searches, and handle chemical reactions.
    253
    repo stars
18. ▌
    rowan · lingxling bundle

    Run cloud-native molecular modeling and drug-design workflows via a Python API, covering pKa prediction, docking, conformer and tautomer ensembles, molecular dynamics, and related small-molecule or protein tasks without local HPC infrastructure.
    253
    repo stars
19. ▌
    simpy · lingxling bundle

    Build discrete-event simulations of systems with processes, queues, resources, and time-based events using the SimPy framework in Python.
    253
    repo stars
20. ▌
    sympy · lingxling bundle

    Provides guidance for using SymPy for exact symbolic mathematics in Python, covering algebra, calculus, equation solving, linear algebra, physics, and code generation.
    253
    repo stars
21. ▌
    depmap · lingxling bundle

    Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.
    253
    repo stars
22. ▌
    flowio · lingxling bundle

    Parse FCS (Flow Cytometry Standard) files v2.0-3.1, extracting events as NumPy arrays, metadata, and channel information, with support for creating and modifying FCS files.
    253
    repo stars
23. ▌
    geniml · lingxling bundle

    Trains machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.
    253
    repo stars
24. ▌
    matlab · lingxling bundle

    Numerical computing with MATLAB and GNU Octave for matrix operations, data analysis, visualization, and scientific computing, including script execution and syntax guidance.
    253
    repo stars
25. ▌
    pathml · lingxling bundle

    Loads and processes whole-slide pathology images, builds spatial graphs, trains deep learning models, and analyzes multiplexed immunofluorescence data across 160+ slide formats.
    253
    repo stars
26. ▌
    plotly · lingxling bundle

    Creates interactive, publication-quality charts with 40+ types, hover tooltips, zoom, and web-embeddable exports for dashboards and exploratory analysis.
    253
    repo stars
27. ▌
    polars · lingxling bundle

    High-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.
    253
    repo stars
28. ▌
    qiskit · lingxling bundle

    Build, optimize, and execute quantum circuits on IBM Quantum hardware or local simulators using Qiskit, including transpilation, primitives, and algorithm libraries.
    253
    repo stars
29. ▌
    scanpy · lingxling bundle

    Runs standard single-cell RNA-seq analysis with Scanpy, covering QC, normalization, dimensionality reduction, clustering, marker identification, visualization, and conversion of R single-cell formats to h5ad.
    253
    repo stars
30. ▌
    scvelo · lingxling bundle

    Analyze RNA velocity in single-cell RNA-seq data with scVelo, estimating cell state transitions from unspliced/spliced mRNA dynamics, inferring trajectory directions, computing latent time, and identifying driver genes.
    253
    repo stars
31. ▌
    adaptyv · lingxling bundle

    Submit protein sequences to the Adaptyv Bio Foundry for experimental characterization (binding, thermostability, expression, fluorescence) and retrieve results using the REST API or Python SDK.
    253
    repo stars
32. ▌
    anndata · lingxling bundle

    Manages annotated data matrices for single-cell genomics, covering creation, I/O, concatenation, and manipulation of AnnData objects in h5ad and zarr formats.
    253
    repo stars
33. ▌
    astropy · lingxling bundle

    Provides guidance on using the Astropy library for astronomy and astrophysics workflows, including units, coordinates, FITS I/O, tables, time, WCS, and cosmology.
    253
    repo stars
34. ▌
    cobrapy · lingxling bundle

    Performs constraint-based metabolic modeling with COBRApy: FBA, FVA, gene knockouts, flux sampling, and SBML model handling for systems biology and metabolic engineering.
    253
    repo stars
35. ▌
    datamol · lingxling bundle

    Pythonic wrapper around RDKit for cheminformatics, simplifying SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, and parallel processing while returning native rdkit.Chem.Mol objects.
    253
    repo stars
36. ▌
    denario · lingxling bundle

    Automates scientific research workflows from data analysis to publication, orchestrating multiple agents for hypothesis generation, methodology development, computational experiments, and LaTeX paper writing.
    253
    repo stars
37. ▌
    lamindb · lingxling bundle

    Manages biological datasets and models with LaminDB, covering setup, artifact registration, querying, lineage tracking, validation, ontology annotation, collections, branches, storage, and workflow integrations.
    253
    repo stars
38. ▌
    matchms · lingxling bundle

    Process and analyze mass spectrometry data with the Matchms Python library, including importing spectra, filtering peaks, calculating similarity scores, and building reproducible analytical workflows.
    253
    repo stars
39. ▌
    medchem · lingxling bundle

    Filters and prioritizes compound libraries in drug discovery using drug-likeness rules, structural alerts, complexity metrics, and a query language.
    253
    repo stars
40. ▌
    molfeat · lingxling bundle

    Convert chemical structures (SMILES or RDKit molecules) into numerical representations for machine learning, covering 100+ featurizers including ECFP, MACCS, descriptors, and pretrained models like ChemBERTa, with support for QSAR modeling and virtual screening.
    253
    repo stars
41. ▌
    onekgpd · lingxling bundle

    Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants, returning variants, carriers, and relatedness with allele frequencies and annotations.
    253
    repo stars
42. ▌
    primekg · lingxling bundle

    Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
    253
    repo stars
43. ▌
    pydicom · lingxling bundle

    Read, write, and modify DICOM medical imaging files, including pixel data extraction, anonymization, format conversion, and compression handling.
    253
    repo stars
44. ▌
    seaborn · lingxling bundle

    Create publication-quality statistical graphics in Python with seaborn, covering relational, distribution, and categorical plots with pandas integration.
    253
    repo stars
45. ▌
    writing · lingxling bundle

    Produces academic papers, literature reviews, grant proposals, and clinical reports with LaTeX formatting and verified citations, using research-lookup and parallel-web skills.
    253
    repo stars