I write about using Unix, R and Programming for Bioinformatics.
I am a Software Engineer at RStudio, working with Hadley Wickham to improve data science tools in R. Previously I have worked on the Bioconductor core team, as a Data Scientist at Explorys and as a Bioinformatician in David Serre's Lab; part of the Genomic Medicine Institute at the Cleveland Clinic.
Covr - Test Coverage for R Packages
Track and report code coverage for your package and (optionally)
upload the results to a coverage service like Codecov (http://codecov.io)
or Coveralls (http://coveralls.io). Code coverage is a measure of the
amount of code being exercised by the tests. It is an indirect measure of
test quality. This package is compatible with any testing methodology or
framework and tracks coverage of both R code and compiled C/C++/Fortran code.
Lintr - Static R Code Analysis
Rex - Friendly Regular Expressions
Gmailr - Access the Gmail RESTful API
Maternal Nutrition Induces Pervasive Gene Expression Changes but No Detectable DNA Methylation Differences in the Liver of Adult Offspring Matthew V. Cannon, David A. Buchner, James Hester, Hadley Miller, Ephraim Sehayek, Joseph H. Nadeau, David Serre
Whole Genome Sequencing of Field Isolates Provides Robust Characterization of Genetic Diversity in Plasmodium vivax. Chan ER, Menard D, David PH, Ratsimbasoa A, Kim S, Chim P, Do C, Witkowski B, Mercereau-Puijalon O, Zimmerman PA, Serre D. PLoS Negl Trop Dis. 2012 Sep;6(9):e1811. Epub 2012 Sep 6.
A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data. Chan ER, Hester J, Kalady M, Xiao H, Li X, Serre D. Genomics. 2011 Oct;98(4):253-9. Epub 2011 Apr 15.
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Serre D, Lee BH, Ting AH. Nucleic Acids Res. 2010 Jan;38(2):391-9. Epub 2009 Nov 11.