├── LICENSE ├── README.md ├── pics_readme ├── Correlation_plot.png ├── correlation_matrix.csv ├── photo1.PNG ├── photo10.PNG ├── photo1A.PNG ├── photo2.PNG ├── photo2A.png ├── photo3.PNG ├── photo5.PNG ├── photo7.PNG ├── photo8.PNG ├── photo9.PNG ├── photo_of_the_folder.PNG ├── phtoto6.PNG └── user_provided.txt ├── repeatprof └── scripts ├── .RData ├── .Rhistory ├── all_corr.R ├── analyze_per_ref.sh ├── bam_analyses.sh ├── clustering_test.R ├── depth_analyser.R ├── encode_var.R ├── fasta_splitter.sh ├── map_reads.sh ├── mk_profiles.R ├── mk_profiles_all.R ├── mk_profiles_ref.R ├── mk_profiles_single.R ├── multi_var_plots.R ├── pileup_basecount.py ├── preparing_bam_to_analyze.sh ├── readme_gen.sh ├── single_copy_calculator.R ├── singlecopy.sh ├── user_groups_maker.R └── var_plots.R /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/johnssproul/RepeatProfiler/HEAD/LICENSE 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