| name | bioconductor-experimenthub |
| description | This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me |
| when_to_use | Use when: Accessing Curated Datasets: Retrieving large files of curated data from experiments, publications, or training courses via the ExperimentHub web service.; Retrieving R Objects: Downloading specific R data objects like SummarizedExperiment, ExpressionSet, or GAlignmentPairs directly into your session.; Interactive Exploration: Interactively querying and exploring available resources using BiocHubsS. Not for: For accessing reference genome annotations, use AnnotationHub because ExperimentHub is focused exclusively on experimental data. |
| user-invocable | false |
ExperimentHub
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 3.2.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Depends: BiocGenerics, AnnotationHub, BiocFileCache
- Imports: S4Vectors, BiocManager, rappdirs
- Install:
BiocManager::install("ExperimentHub")
When to Use
- Accessing Curated Datasets: Retrieving large files of curated data from experiments, publications, or training courses via the
ExperimentHub web service.
- Retrieving R Objects: Downloading specific R data objects like
SummarizedExperiment, ExpressionSet, or GAlignmentPairs directly into your session.
- Interactive Exploration: Interactively querying and exploring available resources using
BiocHubsShiny.
When NOT to Use
- For accessing reference genome annotations, use
AnnotationHub because ExperimentHub is focused exclusively on experimental data.
Data Requirements
- Requires an internet connection to download files initially, which are then cached locally.
- Queries use string terms (e.g., "mus musculus" or "alpineData").
Key Parameters
- localHub: Set to
TRUE in ExperimentHub to use only the local cache and avoid internet queries.
- ask: Set to
FALSE in removeCache to bypass interactive prompts when deleting the cache.
- appname: Used in
rappdirs::user_cache_dir to specify the package name (e.g., "ExperimentHub").
- which: Used in
tools::R_user_dir to specify the directory type (e.g., "cache").
Best Practices
- Use
query to search for specific strings and filter the ExperimentHub object before downloading.
- Check
snapshotDate and use possibleDates to ensure reproducibility with older versions of a snapshot.
- Manage the default caching location using
tools::R_user_dir or by setting the EXPERIMENT_HUB_CACHE environment variable.
Common Pitfalls
- Proxy Issues: Operating behind a proxy blocks downloads; fix by setting the
EXPERIMENT_HUB_PROXY environment variable or using setExperimentHubOption.
- Permission Errors: Sharing a cache across multiple users causes access failures; fix by changing the group permissions of
BiocFileCache.sqlite and BiocFileCache.sqlite.LOCK to g+rw.
- Lost Cache: Upgrading to newer versions changes the default cache location; fix by moving files to the new
tools::R_user_dir location or setting EXPERIMENT_HUB_CACHE.
Alternatives
- AnnotationHub: For retrieving annotation resources rather than experiment data.
- BiocHubsShiny: For a graphical interface to perform the same queries interactively.
Citations
- ExperimentHub Package Authors. ExperimentHub: Access the ExperimentHub Web Service. Bioconductor.
References
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