├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── .travis.yml ├── ChangeLog ├── DESCRIPTION ├── LICENSE ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── bin.R ├── cbioportal_trasefer.R ├── cli.R ├── filter.R ├── format.R ├── future.R ├── handler.R ├── log.R ├── merge.R ├── mhandler.R ├── ngstk.R ├── proteinpaint_transefer.R ├── proteinpaint_utils.R ├── split.R ├── time_stamp.R └── utils.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── inst └── extdata │ ├── bin │ └── demo_bin.sh │ ├── config │ ├── cbioportal.toml │ ├── filter.toml │ ├── handler.toml │ ├── mhandler.toml │ ├── proteinpaint.toml │ └── theme.toml │ ├── demo │ ├── format │ │ ├── -cancer-circrna.txt │ │ ├── common-circrna.txt │ │ ├── hg38-cancer-circrna.txt │ │ ├── hg38-common-circrna.txt │ │ └── hg38_cancer_circrna_mre.txt │ ├── proteinpaint │ │ ├── fusions2pp_fusioncatcher.txt │ │ ├── heatmap_meta_data.txt │ │ ├── heatmap_meta_template.txt │ │ ├── heatmap_mutations.txt │ │ ├── heatmap_sample_group.txt │ │ └── muts2pp_iseq.txt │ └── tools_config.json │ └── tools │ ├── QualityConfirm │ ├── ClassDefine.R │ ├── ClassMethod.R │ ├── README.md │ ├── demo.R │ ├── example │ │ ├── APL1.bam │ │ ├── APL2.bam │ │ ├── APL_panel.bed │ │ ├── te.bam │ │ └── te2.bam │ ├── result │ │ ├── depth │ │ │ └── APL1.bam.depth │ │ ├── fig │ │ │ ├── APL2.bam.countFig.RARA.pdf │ │ │ ├── APL2.bam.countFig.RUNX1.pdf │ │ │ ├── APL2.bam.countFig.SMC1A.pdf │ │ │ ├── APL2.bam.countFig.SMC3.pdf │ │ │ ├── APL2.bam.countFig.STAG2.pdf │ │ │ ├── APL2.bam.countFig.TET2.pdf │ │ │ ├── APL2.bam.countFig.TP53.pdf │ │ │ ├── APL2.bam.countFig.U2AF1.pdf │ │ │ ├── APL2.bam.countFig.USP9X.pdf │ │ │ └── APL2.bam.countFig.WT1.pdf │ │ ├── merge.panel.bed │ │ └── summary │ │ │ ├── APL1.bam.summary.csv │ │ │ ├── APL2.bam.summary.csv │ │ │ ├── analy.all.gene.csv │ │ │ ├── analy.lowreads.region.csv │ │ │ ├── analy.nonreads,region.csv │ │ │ ├── mean.coverage.hist.pdf │ │ │ ├── merged.panel.hist.pdf │ │ │ └── orig.panel.hist.pdf │ └── utils.R │ ├── annovar │ └── create_index.pl │ ├── deseq2 │ ├── README.md │ ├── diffexp.txt │ ├── exp.R │ ├── group.txt │ └── htseq_count │ │ ├── C001.txt │ │ ├── C002.txt │ │ ├── C003.txt │ │ └── C004.txt │ ├── gvmap │ ├── DESCRIPTION │ ├── NAMESPACE │ ├── R │ │ ├── SVGelement.R │ │ ├── addLoc.R │ │ ├── gvmap.R │ │ ├── plotGroup.R │ │ └── sampleEle.R │ ├── README.md │ ├── data │ │ ├── gvmap.config.yaml │ │ └── gvmap.test.txt.gz │ ├── inst │ │ └── extdata │ │ │ └── test_data │ │ │ ├── gvmap.config.yaml │ │ │ ├── gvmap.output.pdf │ │ │ ├── gvmap.output.svg │ │ │ ├── gvmap.test.txt │ │ │ └── gvmap_manual.html │ └── man │ │ └── gvmap.Rd │ └── rbash │ ├── README.md │ ├── build_sqlite │ ├── crawbio │ ├── formatr │ └── sqlite2sql ├── man ├── batch_file.Rd ├── figures │ ├── gvmap_fig1.png │ ├── logo.png │ ├── logo.svg │ └── quality_confirm_fig1.jpg ├── format_filenames.Rd ├── format_pp_meta_age.Rd ├── format_pp_meta_fusions.Rd ├── format_pp_meta_gender.Rd ├── fusions2oncoprinter.Rd ├── fusions2pp.Rd ├── fusions2pp_meta.Rd ├── fusions_filter.Rd ├── get_files_ctime.Rd ├── get_files_mtime.Rd ├── get_pp_samplegroup.Rd ├── get_split_seqs.Rd ├── make_option.Rd ├── merge_table_files.Rd ├── muts2mutation_mapper.Rd ├── muts2oncoprinter.Rd ├── muts2pp.Rd ├── ngstk.Rd ├── opt_parser.Rd ├── par_download.Rd ├── parse_args.Rd ├── parse_args2.Rd ├── print_help.Rd ├── rbin.Rd ├── set_colors.Rd ├── set_tools.Rd ├── show_handlers.Rd ├── show_mhandlers.Rd ├── split_col_data.Rd ├── split_list.Rd ├── split_row_data.Rd ├── split_row_file.Rd ├── supress_any_message.Rd └── time_stamp.Rd ├── ngstk.Rproj ├── tests ├── testthat.R └── testthat │ ├── test_a_utils.R │ ├── test_b_proteinpaint_transefer.R │ ├── test_c_proteinpaint_utils.R │ ├── test_d_filter.R │ ├── test_e_handler.R │ ├── test_f_cbioportal_transefer.R │ ├── test_g_file.R │ ├── test_h_log.R │ ├── test_k_split.R │ ├── test_l_format.R │ ├── test_m_time_stamp.R │ ├── test_n_future.R │ ├── test_o_cli.R │ └── test_p_bin.R └── vignettes └── ngstk.Rmd 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