├── .Rbuildignore ├── .Rproj.user └── CD02ED0 │ ├── cpp-definition-cache │ ├── pcs │ ├── debug-breakpoints.pper │ ├── files-pane.pper │ ├── source-pane.pper │ ├── windowlayoutstate.pper │ └── workbench-pane.pper │ ├── persistent-state │ ├── saved_source_markers │ └── sdb │ ├── prop │ ├── 23C73958 │ ├── 2E63A419 │ ├── 32E011F9 │ ├── 68A9BA79 │ ├── D9AC0466 │ ├── DD5458E2 │ ├── EBA575A7 │ ├── F1C0BA22 │ ├── F78FEF6A │ ├── F854CBB1 │ └── INDEX │ └── s-2ED88DA7 │ ├── 493EA3DC │ └── lock_file ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── reading_functions.R └── util_functions.R ├── README.md ├── example_peak_calling.R ├── man ├── combine.experiments.Rd ├── combined.analysis.Rd ├── data.frame.to.peakC.Rd ├── hello.Rd ├── pairwise.jaccard.Rd ├── plot_C.Rd ├── readMatrix.Rd ├── readMultiColumnFile.Rd ├── readMultiple.Rd ├── readMultipleWig.Rd ├── readqWig.Rd ├── rem.Rd ├── running.Rd └── single.analysis.Rd ├── peakC.Rproj └── tutorial ├── data ├── Hba_cis.txt ├── Hbb_cis.txt ├── alpha-globin_ESC_1_cis.wig ├── alpha-globin_FL_1_cis.wig.gz ├── alpha-globin_FL_2_cis.wig.gz ├── alpha-globin_FL_3_cis.wig.gz ├── alpha-globin_forward_1_chr11_win_1_cis.wig.zip ├── alpha-globin_mESC_1_cis.wig.gz ├── alpha-globin_mESC_2_cis.wig.gz ├── alpha-globin_mESC_3_cis.wig.gz └── peakC_tutorial_Oacyl_6_reps_mappedReads.txt │ ├── set2_viewpoint_1_replicate_1.txt.gz │ ├── set2_viewpoint_1_replicate_2.txt.gz │ ├── set2_viewpoint_1_replicate_3.txt.gz │ ├── set2_viewpoint_1_replicate_4.txt.gz │ ├── set2_viewpoint_1_replicate_5.txt.gz │ └── set2_viewpoint_1_replicate_6.txt.gz ├── library.bib ├── peakC_tutorial.Rmd ├── peakC_tutorial.html ├── peakC_tutorial.pdf └── peakC_tutorial_conflict-20180412-115545.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/deWitLab/peakC/HEAD/.Rbuildignore -------------------------------------------------------------------------------- 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