On Sun, Dec 18, 2022 at 4:07 PM Hao Feng <hxf...@case.edu> wrote: > Hi Bioconductor team, > > We’re developing a package to analyze a `new` type of high-throughput > sequencing data. We have some BAM files ready. We’d like the package to be > able to take BAM files as the input. In addition, to maintain our method’s > statistical rigor, we’d like to implement repeated sampling for multiple > times (a large number). > > This brings concern to a package development, which I’d like to collect > some feedback prior to proceed: > 1. The best practice to use BAM files as the example data? BAM files are > large in general. Although we can use a part of the BAM, instead of the BAM > from the whole genome, as the example data, I still don’t think it’s > feasible to include those external files in the package submission. And due > to the novelty of this sequencing experiment, I don’t think the current > experiment data packages have them. Would you suggest us submitting a new > experiment data package (of several dozen MBs), along with our software > package?
Yes > > 2. Deal with long example run time? Due to repeated sampling and the > handling of BAM files, we suspect our software code examples may take a > long running time. Do you have any suggestions on this so it can pass the > software checking, which is time-bound? > https://contributions.bioconductor.org/long-tests.html We will be happy to help you through any technical obstacles you encounter in preparing either the experiment data submission or the long testing situation. Thank you > > Thank you very much in advance. > > > > > Regards, > Hao > > > --- > Hao Feng, Ph.D. > Assistant Professor in Biostatistics > Department of Population and Quantitative Health Sciences > Case Western Reserve University School of Medicine > Harland Wood Building - Room WG-82T > 10900 Euclid Avenue > SOM / Room G82T > Cleveland, OH 44106-4945 > Phone: 216-368-5510 > Lab website: https://hfenglab.org/ > Official website: http://epbiwww.case.edu/haofeng-phd/ > Email: hxf...@case.edu <mailto:hxf...@case.edu> > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel