Publish data on bioconductor?

[mbuttner]

Dear jdblischak,

I was wondering if you can create a data package on bioconductor containing the processed data. The reason I am asking is that I wrote an R package for the quantification of batch effects (https://github.com/theislab/kBET), for which I created a vignette using your processed data. The guidelines of bioconductor require a separate storage of experimental data and I think that you are certainly unhappy if I am to publish your processed data on bioconductor.
You would certainly help me and it gives you the opportunity to reach a broader audience.

Best regards

[jdblischak]

Hi @mbuttner! Cool method! Thanks for your interest in our project. I'd be happy to help facilitate you and others using our data. Some follow-up questions:

1. What type of package would you prefer? A traditional experiment data package or an ExperimentHub package?
2. What kind of object would you prefer? I am most familiar with the ExpressionSet class, so I would default to this.
3. Which data files do you need easily available for your package? Do you need the reads too or only the molecules (i.e. UMI counts)?

[mbuttner]

Hi @jdblischak! Thanks for your quick reply :) Regarding your questions: 1. I would prefer a traditional experiment data package, but probably your data is already large enough to consider the ExperimentHub instead. 2. I agree with the ExperimentSet Class. 3. I would need the following files: ‘molecules.txt’, ‘annotation.txt’ and ‘quality-single-cells.txt’; i.e. I only need the UMI counts. I thank you a lot for your help!

On 23.01.2018, at 17:28, John Blischak ***@***.***> wrote: Hi @mbuttner <https://github.com/mbuttner>! Cool method! Thanks for your interest in our project. I'd be happy to help facilitate you and others using our data. Some follow-up questions: What type of package <https://www.bioconductor.org/developers/package-guidelines/#package-types> would you prefer? A traditional experiment data package or an ExperimentHub package? What kind of object would you prefer? I am most familiar with the ExpressionSet class, so I would default to this. Which data files do you need easily available for your package? Do you need the reads too or only the molecules (i.e. UMI counts)? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#56 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AXRxAsCYEP-NFkRRmPGDjjsNrtRpOWCrks5tNgiTgaJpZM4RpV9K>.

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