Our team has curated a collection of 107 gene-expression datasets from different sources (e.g., GEO, ArrayExpress) that are saved in a publicly accessible repository (Open Science Framework). All these datasets contain expression levels for the same genes across a wide variety of samples related to breast cancer. We also have metadata and gene information and are storing all this information in SummarizedExperiment objects.

We want to create a Bioconductor/ExperimentHub package or packages that make this data available for analysis by others. Would it be best to create one package for each dataset (107 packages total). Or is there a way to create one package that includes all 107 datasets (each in a separate SummarizedExperiment object)?

Many thanks, and sorry if we missed something in the documentation about this!

107 packages would be a lot! It is certainly possible (and recommended) to implement one package that utilizes ExperimentHub for controlling the download of the datasets. Each summarized experiment object would be a different entry in the ExperimentHub (by a unique entry in a metadata.csv file to add the resource); and you could specialize filtering and querying of ExperimentHub for a particular resource of interest within the one package. Feel free to ask further questions here or at hubs @ bioconductor.org