Questions and Answers for new Bioconductor package authors

• Welcome to the 1st Bioconductor Q&A!
• Please post any questions into the YouTube chat window
• After after a short talk, I will be able to answer them

• Analysis & comprehension of high-throughput genomic data
• Robust software
  • Documented
  • Tested
  • Freely Available
• Reproducible research
• Code reuse and the importance of working together

• To improve your package
• To ensure that your package helps meet the goals of the project
• To help you to know more about other existing packages/objects

• Package guidelines (http://bioconductor.org/developers/package-guidelines/)
• Primer for new package authors (http://bioconductor.org/developers/how-to/buildingPackagesForBioc)
• The support site (https://support.bioconductor.org/)
• The bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel)

• BiocCheck (http://bioconductor.org/packages/devel/bioc/html/BiocCheck.html), install as follows:

source("http://bioconductor.org/biocLite.R")
biocLite("BiocCheck")
library(BiocCheck)

• Code reuse
• Good documentation - Everyone must understand vignette.
• Why do people care about how my code looks? (code readability)

• Our svn codebase is public
• Many journals like if your software is already online
• Ultimately: you have to check with the specific journals (It's their policies that matter)

• Don't panic - the process is meant to help you.
• Build and check your package (using Bioc ' devel'!)

R CMD build MyPkg
R CMD check MyPkg_0.99.0.tar.gz
R CMD BiocCheck MyPkg_0.99.0.tar.gz

• Put packages into the tracker (https://tracker.bioconductor.org/issue558)
• Don't create extra issues for new tarballs

• Bioconductor is supported in part by these grants:

  NHGRI / NIH U41HG004059

  NSF 1247813