Directories
¶
| Path | Synopsis |
|---|---|
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Package cache implements a content-addressable local blob cache for hapiq.
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Package cache implements a content-addressable local blob cache for hapiq. |
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Package downloaders provides a pluggable interface for downloading datasets from various scientific data repositories with comprehensive metadata tracking and provenance information.
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Package downloaders provides a pluggable interface for downloading datasets from various scientific data repositories with comprehensive metadata tracking and provenance information. |
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biostudies
Package biostudies downloads datasets from EBI BioStudies (https://www.ebi.ac.uk/biostudies).
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Package biostudies downloads datasets from EBI BioStudies (https://www.ebi.ac.uk/biostudies). |
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common
Package common provides shared utilities for downloader implementations including filesystem operations, progress tracking, and user interaction.
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Package common provides shared utilities for downloader implementations including filesystem operations, progress tracking, and user interaction. |
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ensembl
Package ensembl provides download functionality for Ensembl Genomes datasets.
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Package ensembl provides download functionality for Ensembl Genomes datasets. |
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experimenthub
Package experimenthub implements a hapiq downloader for Bioconductor's ExperimentHub.
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Package experimenthub implements a hapiq downloader for Bioconductor's ExperimentHub. |
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figshare
Package figshare provides download functionality for different Figshare dataset types including articles, collections, and projects with comprehensive file handling.
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Package figshare provides download functionality for different Figshare dataset types including articles, collections, and projects with comprehensive file handling. |
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geo
Package geo provides download functionality for different GEO dataset types using NCBI E-utilities for metadata discovery and FTP for file downloads.
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Package geo provides download functionality for different GEO dataset types using NCBI E-utilities for metadata discovery and FTP for file downloads. |
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hca
Package hca downloads count matrices and processed files from the Human Cell Atlas Data Portal via the Azul service API.
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Package hca downloads count matrices and processed files from the Human Cell Atlas Data Portal via the Azul service API. |
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scanpy
Package scanpy implements a hapiq downloader for the curated datasets shipped with scanpy.datasets (the network-fetched ones; package-bundled datasets are out of scope).
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Package scanpy implements a hapiq downloader for the curated datasets shipped with scanpy.datasets (the network-fetched ones; package-bundled datasets are out of scope). |
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scperturb
Package scperturb downloads datasets from the scPerturb collection (Peidli et al., Nature Methods 2024), a standardised compendium of single-cell perturbation studies.
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Package scperturb downloads datasets from the scPerturb collection (Peidli et al., Nature Methods 2024), a standardised compendium of single-cell perturbation studies. |
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sra
Package sra downloads raw sequencing reads (FASTQ) from the ENA/SRA via EBI's public HTTPS mirror.
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Package sra downloads raw sequencing reads (FASTQ) from the ENA/SRA via EBI's public HTTPS mirror. |
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url
Package url implements a hapiq downloader that fetches a single file directly from an arbitrary HTTP(S) URL.
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Package url implements a hapiq downloader that fetches a single file directly from an arbitrary HTTP(S) URL. |
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vcp
Package czi downloads datasets from the CZI Virtual Cell Platform (VCP).
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Package czi downloads datasets from the CZI Virtual Cell Platform (VCP). |
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zenodo
Package zenodo provides download functionality for Zenodo datasets with progress tracking, file management, and error handling.
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Package zenodo provides download functionality for Zenodo datasets with progress tracking, file management, and error handling. |
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Package manifest defines a YAML-based DSL for declaring datasets to download and verify in bulk.
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Package manifest defines a YAML-based DSL for declaring datasets to download and verify in bulk. |
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