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
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Use bioconductor-experimenthub to query ExperimentHub for curated experimental datasets matching [research topic, organism, and desired R object or data type], and return suitable resources with their metadata and a reproducible snapshot-date recommendation; use the existing R environment and cache settings, with internet access required for resources not already cached.
Required inputs
[research topic, organism, and desired R object or data type]
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SKILL.md
name: bioconductor-experimenthubdescription: 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 mewhen_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.
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.
This skill is the knowledge layer — when, why, and how to use experimenthub. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.