1. General SNP Analysis packages
   1. GWASTools
      1. examples
         1. Affymetrix.pdf
         2. Formats.pdf
         3. DataCleaning.pdf
         4. VCF.pdf
      2. GWASdata
   2. SNPRelate
      1. SNPRelate.pdf
      2. SNPRelateTutorial.pdf
   3. adegenet
      1. adegenet.pdf
      2. tutorial
      3. tutorial_sPCA
      4. tutorial_daPC
   4. SKAT
      1. SKAT.pdf
      2. SKAT_VIG.pdf
   5. AssotesteR
      1. AssotesteR.pdf
2. Annotation Packages
   1. postgwas
      1. postgwas.pdf
      2. postgwas faq.pdf
   2. rsnps
      1. rsnps_vignette.pdf
3. Plotting Packages
   1. d3Network
      1. d3Network.pdf
      2. examples
   2. diagram
      1. diagram.pdf
   3. HiveR
      1. HiveR.pdf
      2. HiveR_vig.pdf
   4. rCharts
      1. rCharts.pdf
      2. examples
4. Genomic Data Mining / Computational Analysis Packages
   1. bigrf
      1. bigrf.pdf
   2. boostr
      1. boostr_vignette_part2
      2. boostr_vignette_part1
   3. parallelComputeR
      1. parallel-parametric_bootstrap example.pdf
5. Presenting Research Packages
   1. scdocR
      1. scdocR_vignette.pdf
   2. slidify
      1. examples
         1. Slidify_methods_presentation_example.pdf
      2. example presentations
         1. one of many examples...
6. New or Relevant Pathway Analysis Packages
   1. GSAgm
      1. PCGammaR.pdf
   2. PAGWAS
      1. PAGWAS.pdf
   3. PCGSE
      1. gplm-examples.pdf
      2. PCGSE.pdf
   4. TcGSA
      1. TcGSA.pdf
   5. CePa
      1. Examples
         1. analysis-p53.pdf
         2. parsing-PID-pathway-data.pdf
      2. CePa_Vignette.pdf
   6. minPtest
      1. minPtest.pdf
      2. minPtest_vignette.pdf
   7. topologyGSA
      1. topologyGSA.pdf
   8. dna
      1. dna.pdf
      2. dna_vignette.pdf