Files in JhuangLab/ngstk
Next-Generation Sequencing (NGS) Data Analysis Toolkit

.Rbuildignore
.gitattributes
.gitignore
.travis.yml
ChangeLog
DESCRIPTION
LICENSE
Makefile
NAMESPACE
NEWS.md R/bin.R R/cbioportal_trasefer.R R/cli.R R/filter.R R/format.R R/future.R R/handler.R R/log.R R/merge.R R/mhandler.R R/ngstk.R R/proteinpaint_transefer.R R/proteinpaint_utils.R R/split.R R/time_stamp.R R/utils.R README.Rmd README.md
_pkgdown.yml
inst/extdata/bin/demo_bin.sh
inst/extdata/config/cbioportal.toml
inst/extdata/config/filter.toml
inst/extdata/config/handler.toml
inst/extdata/config/mhandler.toml
inst/extdata/config/proteinpaint.toml
inst/extdata/config/theme.toml
inst/extdata/demo/format/-cancer-circrna.txt
inst/extdata/demo/format/common-circrna.txt
inst/extdata/demo/format/hg38-cancer-circrna.txt
inst/extdata/demo/format/hg38-common-circrna.txt
inst/extdata/demo/format/hg38_cancer_circrna_mre.txt
inst/extdata/demo/proteinpaint/fusions2pp_fusioncatcher.txt
inst/extdata/demo/proteinpaint/heatmap_meta_data.txt
inst/extdata/demo/proteinpaint/heatmap_meta_template.txt
inst/extdata/demo/proteinpaint/heatmap_mutations.txt
inst/extdata/demo/proteinpaint/heatmap_sample_group.txt
inst/extdata/demo/proteinpaint/muts2pp_iseq.txt
inst/extdata/demo/tools_config.json
inst/extdata/tools/QualityConfirm/ClassDefine.R inst/extdata/tools/QualityConfirm/ClassMethod.R inst/extdata/tools/QualityConfirm/README.md inst/extdata/tools/QualityConfirm/demo.R
inst/extdata/tools/QualityConfirm/example/APL1.bam
inst/extdata/tools/QualityConfirm/example/APL2.bam
inst/extdata/tools/QualityConfirm/example/APL_panel.bed
inst/extdata/tools/QualityConfirm/example/te.bam
inst/extdata/tools/QualityConfirm/example/te2.bam
inst/extdata/tools/QualityConfirm/result/depth/APL1.bam.depth
inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.RARA.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.RUNX1.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.SMC1A.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.SMC3.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.STAG2.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.TET2.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.TP53.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.U2AF1.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.USP9X.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.WT1.pdf
inst/extdata/tools/QualityConfirm/result/merge.panel.bed
inst/extdata/tools/QualityConfirm/result/summary/APL1.bam.summary.csv
inst/extdata/tools/QualityConfirm/result/summary/APL2.bam.summary.csv
inst/extdata/tools/QualityConfirm/result/summary/analy.all.gene.csv
inst/extdata/tools/QualityConfirm/result/summary/analy.lowreads.region.csv
inst/extdata/tools/QualityConfirm/result/summary/analy.nonreads,region.csv
inst/extdata/tools/QualityConfirm/result/summary/mean.coverage.hist.pdf inst/extdata/tools/QualityConfirm/result/summary/merged.panel.hist.pdf inst/extdata/tools/QualityConfirm/result/summary/orig.panel.hist.pdf inst/extdata/tools/QualityConfirm/utils.R
inst/extdata/tools/annovar/create_index.pl
inst/extdata/tools/deseq2/README.md
inst/extdata/tools/deseq2/diffexp.txt
inst/extdata/tools/deseq2/exp.R
inst/extdata/tools/deseq2/group.txt
inst/extdata/tools/deseq2/htseq_count/C001.txt
inst/extdata/tools/deseq2/htseq_count/C002.txt
inst/extdata/tools/deseq2/htseq_count/C003.txt
inst/extdata/tools/deseq2/htseq_count/C004.txt
inst/extdata/tools/gvmap/DESCRIPTION
inst/extdata/tools/gvmap/NAMESPACE
inst/extdata/tools/gvmap/R/SVGelement.R inst/extdata/tools/gvmap/R/addLoc.R inst/extdata/tools/gvmap/R/gvmap.R inst/extdata/tools/gvmap/R/plotGroup.R inst/extdata/tools/gvmap/R/sampleEle.R inst/extdata/tools/gvmap/README.md
inst/extdata/tools/gvmap/data/gvmap.config.yaml
inst/extdata/tools/gvmap/data/gvmap.test.txt.gz
inst/extdata/tools/gvmap/inst/extdata/test_data/gvmap.config.yaml
inst/extdata/tools/gvmap/inst/extdata/test_data/gvmap.output.pdf
inst/extdata/tools/gvmap/inst/extdata/test_data/gvmap.output.svg
inst/extdata/tools/gvmap/inst/extdata/test_data/gvmap.test.txt
inst/extdata/tools/gvmap/inst/extdata/test_data/gvmap_manual.html
inst/extdata/tools/gvmap/man/gvmap.Rd
inst/extdata/tools/rbash/README.md
inst/extdata/tools/rbash/build_sqlite
inst/extdata/tools/rbash/crawbio
inst/extdata/tools/rbash/formatr
inst/extdata/tools/rbash/sqlite2sql
man/batch_file.Rd
man/figures/gvmap_fig1.png
man/figures/logo.png
man/figures/logo.svg
man/figures/quality_confirm_fig1.jpg
man/format_filenames.Rd man/format_pp_meta_age.Rd man/format_pp_meta_fusions.Rd man/format_pp_meta_gender.Rd man/fusions2oncoprinter.Rd man/fusions2pp.Rd man/fusions2pp_meta.Rd man/fusions_filter.Rd man/get_files_ctime.Rd man/get_files_mtime.Rd man/get_pp_samplegroup.Rd man/get_split_seqs.Rd man/make_option.Rd man/merge_table_files.Rd man/muts2mutation_mapper.Rd man/muts2oncoprinter.Rd man/muts2pp.Rd man/ngstk.Rd man/opt_parser.Rd man/par_download.Rd man/parse_args.Rd man/parse_args2.Rd man/print_help.Rd man/rbin.Rd man/set_colors.Rd man/set_tools.Rd man/show_handlers.Rd man/show_mhandlers.Rd man/split_col_data.Rd man/split_list.Rd man/split_row_data.Rd man/split_row_file.Rd man/supress_any_message.Rd man/time_stamp.Rd
ngstk.Rproj
tests/testthat.R tests/testthat/test_a_utils.R tests/testthat/test_b_proteinpaint_transefer.R tests/testthat/test_c_proteinpaint_utils.R tests/testthat/test_d_filter.R tests/testthat/test_e_handler.R tests/testthat/test_f_cbioportal_transefer.R tests/testthat/test_g_file.R tests/testthat/test_h_log.R tests/testthat/test_k_split.R tests/testthat/test_l_format.R tests/testthat/test_m_time_stamp.R tests/testthat/test_n_future.R tests/testthat/test_o_cli.R tests/testthat/test_p_bin.R vignettes/ngstk.Rmd
JhuangLab/ngstk documentation built on Nov. 23, 2018, 7:34 p.m.