Bioconductor Experimenthub

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

• Homepage: https://bioconductor.org/packages/ExperimentHub
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html

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