├── .Rbuildignore ├── .gitignore ├── Arabipodsis_analysis.R ├── DESCRIPTION ├── DevelopmentHell.R ├── DevelopmentHell_FixMin.R ├── NAMESPACE ├── PicMin.Rproj ├── R └── PicMin_functions.R ├── README.md ├── WZA_analysis ├── 2D_SteppingStone.wza.csv ├── Analyse_WZA_results.R ├── WZA_results_plot.FixMin.pdf ├── WZA_results_plot.pdf ├── all_results_r10000.7sets.FixMin.csv ├── all_results_r10000.7sets.FixMin099.csv ├── all_results_r10000.7sets.csv ├── all_results_r500000.csv ├── plot_WZA_results.R ├── s0.003 │ ├── BC_Map.wza.csv │ ├── cline.wza.csv │ └── trunc.wza.csv └── s0.0136 │ ├── BC_Map.wza.csv │ ├── cline.wza.csv │ └── trunc.wza.csv ├── genomeAnalysis ├── Rplot.pdf ├── combinedPlot.pdf ├── demoPlot.pdf ├── genome_analysis_3-7.FixMin.csv └── genome_analysis_3-7.csv ├── man ├── EmpiricalPs.Rd ├── GenerateNullData.Rd ├── PicMin.Rd └── orderStatsPValues.Rd └── vignettes ├── Arabidopsis-vignette.Rmd ├── Arabidopsis_ManhattanPlot.png ├── lineage_1.csv ├── lineage_2.csv ├── lineage_3.csv ├── 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