Software

1. GitHub repositories (www.r-pkg.org, rdocumentation, r-universe)

   gaawr2 (manual, news, vignette, Articles: web), https://cran.r-project.org/package=gaawr2

   pQTLdata (manual, news, vignette), https://cran.r-project.org/package=pQTLdata

   pQTLtools (manual, news, vignette, Articles: LocusZoom.js, bioconductor, snakemake)

   R based on R packages

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

   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. Miscellaneous notes
   • I have converted some functionality of my programs (as 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.
   • 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
   • Mixed models
     • 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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