Bioconductor / CRAN release ?

[bvieth]

Dear Koen,

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

Kind regards
Beate

[koenvandenberge]

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]

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]

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).