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ropensci / tidyqpcr

quantitative PCR analysis in the tidyverse
https://docs.ropensci.org/tidyqpcr/
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Include as exported data sets the data from 10.1016/j.ymeth.2012.08.011 #198

Closed ramiromagno closed 4 months ago

ramiromagno commented 1 year ago

Hi @ewallace,

I would like to include data from dx.doi.org/10.1016/j.ymeth.2012.08.011 in {tidyqpcr}:

File Size
Data_Vermeulen_A.xls 5.7M
Data_Vermeulen_B.xls 5.7M
Data_Vermeulen_C.xls 5.7M
Data_Vermeulen_D.xls 5.7M
technical_datasets.xls 795K

I think these data could be really useful for testing baseline subtraction and other processing methodologies.

Given that:

We could perhaps add it as raw data to data-raw/, and then include it as exported data sets (i.e. tibbles) that would be readily available for testing and examples. We could also make a companion data package, and make {tidyqpcr} depend on that...

ramiromagno commented 1 year ago

I just put together an R data package for the Vermeulen data: https://github.com/ramiromagno/vermeulen.

ramiromagno commented 1 year ago

This one might be useful too: https://github.com/ramiromagno/ruijter

ramiromagno commented 1 year ago

vermeulen is now on CRAN.

ramiromagno commented 1 year ago

{ruijter} is on its way to CRAN.

ewallace commented 4 months ago

Hi @ramiromagno I am just getting back to some maintenance updates on tidyqpcr after a long hiatus and silence. Are you still interested in helping to tie some of these into tidyqpcr?

ramiromagno commented 4 months ago

Hi @ewallace:

Yes! It's funny you're getting back at this now because I am right now finishing a set of R data packages that provide a bunch of qPCR data sets:

ewallace commented 4 months ago

@ramiromagno that looks very cool, good to be back in touch.

It looks like your packages already do the pre-tidying of the data?

How were you thinking of fitting these together with tidyqpcr?

ramiromagno commented 4 months ago

I was thinking of using these datasets for testing tidyqpcr algorithms. So we could use these data packages as dependencies, namely add them to Suggests (because we'd use them only in unit tests...?)?

ramiromagno commented 4 months ago

Hi @ewallace:

Originally, I planned to include a set of these data in tidyqpcr for testing purposes. However, I've since resolved this matter by integrating these datasets into separate R packages. Therefore, it's now feasible to rely on them if necessary. As a result, I will now close this issue.