├── .gitignore ├── .gitmodules ├── .travis.yml ├── INSTALL ├── INSTALL.pl ├── README.md ├── ViewBS ├── ViewBSdocker ├── .path_note ├── Dockerfile ├── README.md └── README_bak.md ├── conda ├── conda_upload.md ├── conda_upload.sh └── meta.yaml ├── data ├── bsseeker_CGmap.tab ├── check_issue43 │ ├── README.md │ └── step1_MethCoverage.sh ├── check_issue44 │ └── README.md ├── chk_issue.sh ├── chk_issue25 │ ├── ViewBS │ ├── howto_configure_perl_env.md │ └── test_cmd.sh ├── chk_issue28.sh ├── chk_issue_install_perl.nohup ├── chk_issue_install_perl.sh ├── chk_issues39 │ └── README.md ├── chk_perl_version.pl ├── chk_pull24.sh ├── chk_pull24.tab ├── environment_module_list.txt └── test_data │ ├── Rplots.pdf │ ├── gener_test_data.sh │ ├── test_WT.tab.gz │ └── test_WT.tab.gz.tbi ├── doc ├── TODO ├── code_change_note.txt ├── doc4main_help.txt ├── pod4help_BisNonConvRate.txt ├── pod4help_MethCoverage.txt ├── pod4help_MethGeno.txt ├── pod4help_MethGlobalLev.txt ├── pod4help_MethHeatmap.txt ├── pod4help_MethLevDist.txt ├── pod4help_MethOneRegion.txt └── pod4help_MethOverRegion.txt ├── environment.yaml ├── ext_tools └── cpanm ├── image ├── BisNonConversionRate_example1.png ├── CHG_hypo_DMR_drm12cmt23_to_WT_MethHeatmap_CHG.png ├── GlobalMethLev_example1.png ├── GlobalMethLev_example2.png ├── Header_bioinfoCore.png ├── MethHeatmap_hist.png ├── MethOneRegion.png ├── MethOneRegion_example1.png ├── MethOneRegion_example2.png ├── ViewBS_workflow.png ├── bis_TE_chr1_sample_MethOverRegion_CHG.png ├── bis_geno_sample_MethGeno_CHH.PNG ├── bis_methOverRegion_5rank.png ├── methCoverage_example1.PNG ├── methLevDist_example1.PNG ├── methOverRegion_TE.png └── plot2by2.png ├── lib ├── Meth │ ├── BisNonConvRate.R │ ├── BisNonConvRate.pm │ ├── Coverage.R │ ├── Coverage.pm │ ├── Geno.R │ ├── Geno.pm │ ├── Geno_bak.R │ ├── GlobalLev.R │ ├── GlobalLev.pm │ ├── Heatmap.R │ ├── Heatmap.pm │ ├── LevDist.R │ ├── LevDist.pm │ ├── LevDist_BACKUP_28361.pm │ ├── LevDist_BACKUP_28443.pm │ ├── LevDist_BACKUP_28535.pm │ ├── LevDist_BACKUP_28830.pm │ ├── LevDist_BASE_28361.pm │ ├── LevDist_BASE_28443.pm │ ├── LevDist_BASE_28535.pm │ ├── LevDist_BASE_28830.pm │ ├── LevDist_LOCAL_28361.pm │ ├── LevDist_LOCAL_28443.pm │ ├── LevDist_LOCAL_28535.pm │ ├── LevDist_LOCAL_28830.pm │ ├── LevDist_REMOTE_28361.pm │ ├── LevDist_REMOTE_28443.pm │ ├── LevDist_REMOTE_28535.pm │ ├── LevDist_REMOTE_28830.pm │ ├── OneRegion.R │ ├── OneRegion.pm │ ├── OverRegion.R │ ├── OverRegion.pm │ └── Sample.pm ├── SubCmd │ ├── BisNonConvRate.pm │ ├── CommonArgument.pm │ ├── GlobalMethLev.pm │ ├── MethCoverage.pm │ ├── MethGeno.pm │ ├── MethHeatmap.pm │ ├── MethLevDist.pm │ ├── MethOneRegion.pm │ └── MethOverRegion.pm └── scripts │ ├── .bsseeker2bismark.pl.swp │ ├── brat2bismark.pl │ ├── bsseeker2bismark.pl │ ├── gff2tab.pl │ ├── install.sh │ ├── install_R_packages.R │ └── mer_fig.R └── license.txt /.gitignore: -------------------------------------------------------------------------------- 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