[Bioc-devel] Best practices to load data for vignette/tests
You could see if there is any existing data already in Bioconductor for use with your package. That would be preferable. http://bioconductor.org/packages/release/BiocViews.html#___Software searching for fastq - you could see what data ShortRead, seqTools, and FastqCleaner similarly you could also search for rna-seq packages to see if any of their data is appropriate. There are also a number of experiment data packages that may provide the data format you are in need of. http://bioconductor.org/packages/release/BiocViews.html#___ExperimentData You could search here as well. Lastly, Bioconductor has an experimentHub for storing large data files. You can search interactively in R or the web API interface here: https://experimenthub.bioconductor.org/ If none of those location provide data currently in Bioconductor that is suitable for your package, You can submit your own data to the ExperimentHub. http://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html You could download directly but this could be time consuming depending on internet connections and download speeds. The Bioconductor hubs provide a caching mechanism so it is only downloaded once and then it remembers where the file is on the system for later use. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Julien Wollbrett <julien.wollbrett at unil.ch>
Sent: Tuesday, January 22, 2019 8:57:23 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Best practices to load data for vignette/tests
Sent: Tuesday, January 22, 2019 8:57:23 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Best practices to load data for vignette/tests
Hi everyone, I am currently working on a R package called BgeeCall allowing to automatically generate present/absent expression calls from any RNA-Seq fastq files as long as the species is present in Bgee (https://bgee.org/) . The package is almost ready and I am currently writing the vignette and some tests. This package can be seen as a workflow taking as input one transcriptome and at least one fastq file. My question is how can I import these 2 files to run the vignette/tests? They are too big to be part of my package. Can I directly download them from SRA and ensembl (or from my own server)? Do I need to create a dataset that will be loaded by my package for this kind of raw and publicly available data? Do you know if I could reuse some already existing dataset? I am interested to any best practices infomation. Thank you for your answers. Best Regards, Julien _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.