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statOmics / zingeR

zero-inflated negative binomial gene expression in R
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Bioconductor / CRAN release ? #6

Open bvieth opened 5 years ago

bvieth commented 5 years ago

Dear Koen,

do you have any plans to release zingeR on Bioconductor or CRAN in the near future ?

Kind regards Beate

koenvandenberge commented 5 years ago

Hi Beate,

Congrats on your recent paper on comparing single-cell pipelines; very interesting work. I am not planning to submit zingeR to Bioconductor nor CRAN. Would that be useful to you?

Best, Koen

bvieth commented 5 years ago

Hey Koen, Thank you very much :) Actually, yes that would be useful. Bioconductor only allows for dependencies hosted on Bioconductor or CRAN, not github, and I would like to move powsimR form github to Bioconductor. An option for me would be to incorporate your source code into my package directly, if that is ok for you ? Of course I would cite it accordingly.

Best, Beate

koenvandenberge commented 5 years ago

Hi Beate, My apologies for being late at getting back at this. For now I would suggest to incorporate the function in your package, but to print a message to clearly state whenever it's used. Here is an example of what Mike Love is doing in DESeq2 when ashr is being used: https://github.com/mikelove/DESeq2/blob/master/R/lfcShrink.R#L441-L443

Note that you should only need to incorporate the zeroWeightsLS function; the other functions are already incorporated into zinbwave (which is a Bioconductor package).