scitex-dataset

Getting Started

  • Installation
    • Requirements
    • Basic Installation
    • Development Installation
    • Optional Dependencies
    • Verification
  • Quickstart
    • Install
    • Python API
    • CLI
    • Configuration
    • Next steps

User Guide

  • CLI Reference
    • Configuration precedence
    • Legacy aliases (hidden, exit code 2)
    • Live command tree
  • Data Sources
    • Catalog sources
      • OpenNeuro — BIDS neuroimaging
      • DANDI Archive — NWB neurophysiology
      • PhysioNet — physiological waveforms
      • Zenodo — general scientific data (CERN)
      • Figshare — research data sharing
      • OpenML — ML datasets and benchmarks
      • MoleculeNet — molecular ML benchmarks
      • GEO — Gene Expression Omnibus (NCBI)
      • ChEMBL — bioactivity (EBI)
      • ClinicalTrials.gov — interventional / observational studies
    • On-demand source
      • HuggingFace Hub
    • Local Database

API Reference

  • scitex_dataset API Reference
    • db_build()
    • db_search()
    • db_show_stats()
    • filter_results()
    • list_sources()
    • openneuro_fetch()
    • dandi_fetch()
    • physionet_fetch()
    • gin_fetch()
    • gin_search()
    • gin_info()
    • gin_download()
    • zenodo_fetch()
    • figshare_fetch()
    • openml_fetch()
    • moleculenet_fetch()
    • geo_fetch()
    • chembl_fetch()
    • clinicaltrials_fetch()
    • huggingface_fetch()
    • huggingface_search()
    • huggingface_info()
    • huggingface_download_file()
    • download_dataset()
    • Search Module
      • search_datasets()
      • sort_datasets()
    • Database Module
      • build()
      • update()
      • search()
      • get_stats()
      • get_db_path()
      • clear()
    • Neuroscience Sources
      • OpenNeuro
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
      • DANDI
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
      • PhysioNet
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
    • General Sources
      • Zenodo
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
      • Figshare
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
      • OpenML
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
      • HuggingFace Hub
        • Local-state layout
        • fetch_dataset()
        • search_datasets()
        • search_hub()
        • fetch_all_datasets()
        • format_dataset()
        • dataset_info()
        • download_file()
    • Biology Sources
      • GEO
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
    • Pharmacology Sources
      • MoleculeNet
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
      • ChEMBL
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
    • Medical Sources
      • ClinicalTrials.gov
        • fetch_datasets()
        • fetch_all_datasets()
        • format_dataset()
    • CLI
      • _repositories_block()
scitex-dataset
  • Overview: module code

All modules for which code is available

  • scitex_dataset
    • scitex_dataset._api
    • scitex_dataset._cli
    • scitex_dataset.biology.geo
    • scitex_dataset.database
    • scitex_dataset.general.figshare
    • scitex_dataset.general.huggingface
    • scitex_dataset.general.openml
    • scitex_dataset.general.zenodo
    • scitex_dataset.medical.clinicaltrials
    • scitex_dataset.neuroscience.dandi
    • scitex_dataset.neuroscience.gin
    • scitex_dataset.neuroscience.openneuro
    • scitex_dataset.neuroscience.physionet
    • scitex_dataset.pharmacology.chembl
    • scitex_dataset.pharmacology.moleculenet
    • scitex_dataset.search

© Copyright 2025, Yusuke Watanabe.

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