Software

1. GitHub repositories

   gaawr2 (manual, news, vignette), Articles: web

   pQTLdata (manual, news, vignette)

   pQTLtools (manual, news, vignette), Articles: ExpressionSet/SummarizedExperiment, LocusZoom.js, SCALLOP-Caprion, bioconductor, snakemake, spectrum

   R (www.r-pkg.org, https://www.rdocumentation.org/) based on R packages

   • gap, https://cran.r-project.org/package=gap
     • jss
     • manual, news
     • shinygap, vignette
   • gap.datasets
   • kinship (vignette)
   • lmm (vignette)
   • pan (vignette)
   • tdthap (vignette)

   Haplotype analysis based on C programs

   miscellaneous collections based on miscellaneous programs

2. JumpStart sites
   • Bioconductor contribution, https://contributions.bioconductor.org/index.html
   • CRAN submission, https://cran.r-project.org/submit.html
   • R Contributor Site, https://contributor.r-project.org/
   • R Developer Page, https://developer.r-project.org/

3. I have converted some functionality of my programs (most are on the Rockefeller list of genetic software), implemented new functions or maintained packages by colleagues into R. as reported in gap: Genetic Analysis Package. I also made a University of London LaTeX thesis class, together with Endnote genetic reference library and keep some notes on MFC programming, some programs for genetic data analysis and R/S counterpart.

4. The examples provided for SAS, Stata and R can be considered as extension to those in Genetic dissection of complex traits In silico: approaches, problems and solutions.
   • SAS programs
   • Stata programs
5. My work on mixed models is described in the following papers
   • Mixed-effects Cox models of alcohol dependence in extended families
   • Mixed modeling with whole genome data
   • Bayesian linear mixed models with polygenic effects

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