Downloading count matrix for full recount3 dataset
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Ben • 0
@2b32c5d6
Last seen 3 months ago
United States

Is there an aggregated file for downloading all the metadata or all gene-level counts for the entire recount3 dataset? Or is the recommended way to do so just to iterate over all the projects in available_projects()?

If the latter, is there a rate limit guideline for requests that should be followed?

recount3 • 182 views
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@lcolladotor
Last seen 20 days ago
United States

Hi,

We decided against providing a full gene count matrix object (or exon or exon-exon junction) since you have to remake them every time you update the resource, plus they'd be huge and likely not many would use them. For example, many users asked us to split the GTEx and TCGA data in recount2 and provide ways to download the data from just 1 tissue.

So yes, you'll have to iterate over all the projects.

As for downloading metadata, that's what I did myself at https://github.com/LieberInstitute/recount3-docs/blob/master/study-explorer/obtain_abstracts.R. You might want to use https://github.com/LieberInstitute/recount3-docs/blob/master/study-explorer/projects_meta.Rdata.

As for rate limitations, let's try and see what happens. I can forward this request to SciServer (the data host) if you run into issues.

Best, Leo

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Perhaps we should reconsider this. We could provide a single file as a collection. Let’s talk offline.

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That's fair, thanks for your help!

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