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

ChangeLog
README.md
NAMESPACE
DESCRIPTION
MD5
LICENSE
inst/doc/ngstk.R
inst/doc/ngstk.html
inst/doc/ngstk.Rmd
inst/extdata/config/cbioportal.toml
inst/extdata/config/theme.toml
inst/extdata/config/hander.toml
inst/extdata/config/filter.toml
inst/extdata/config/proteinpaint.toml
inst/extdata/config/mhander.toml
inst/extdata/tools/gvmap/README.md
inst/extdata/tools/gvmap/NAMESPACE
inst/extdata/tools/gvmap/DESCRIPTION
inst/extdata/tools/gvmap/R/plotGroup.R inst/extdata/tools/gvmap/R/sampleEle.R inst/extdata/tools/gvmap/R/SVGelement.R inst/extdata/tools/gvmap/R/gvmap.R inst/extdata/tools/gvmap/R/addLoc.R
inst/extdata/tools/gvmap/data/gvmap.config.yaml
inst/extdata/tools/gvmap/man/gvmap.Rd
inst/extdata/tools/gvmap/inst/extdata/test_data/gvmap_manual.html
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/QualityConfirm/demo.R inst/extdata/tools/QualityConfirm/utils.R inst/extdata/tools/QualityConfirm/README.md inst/extdata/tools/QualityConfirm/ClassMethod.R inst/extdata/tools/QualityConfirm/ClassDefine.R
inst/extdata/tools/QualityConfirm/example/APL2.bam
inst/extdata/tools/QualityConfirm/example/te.bam
inst/extdata/tools/QualityConfirm/example/APL_panel.bed
inst/extdata/tools/QualityConfirm/example/APL1.bam
inst/extdata/tools/QualityConfirm/example/te2.bam
inst/extdata/tools/QualityConfirm/result/merge.panel.bed
inst/extdata/tools/QualityConfirm/result/depth/APL1.bam.depth
inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.STAG2.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.USP9X.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.SMC3.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.RARA.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.WT1.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.TP53.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.TET2.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.SMC1A.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.U2AF1.pdf inst/extdata/tools/QualityConfirm/result/fig/APL2.bam.countFig.RUNX1.pdf
inst/extdata/tools/QualityConfirm/result/summary/APL1.bam.summary.csv
inst/extdata/tools/QualityConfirm/result/summary/orig.panel.hist.pdf inst/extdata/tools/QualityConfirm/result/summary/mean.coverage.hist.pdf
inst/extdata/tools/QualityConfirm/result/summary/APL2.bam.summary.csv
inst/extdata/tools/QualityConfirm/result/summary/merged.panel.hist.pdf
inst/extdata/tools/QualityConfirm/result/summary/analy.lowreads.region.csv
inst/extdata/tools/QualityConfirm/result/summary/analy.all.gene.csv
inst/extdata/tools/QualityConfirm/result/summary/analy.nonreads,region.csv
inst/extdata/demo/tools_config.json
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/format/common-circrna.txt
inst/extdata/demo/format/-cancer-circrna.txt
inst/extdata/demo/proteinpaint/muts2pp_iseq.txt
inst/extdata/demo/proteinpaint/heatmap_meta_data.txt
inst/extdata/demo/proteinpaint/fusions2pp_fusioncatcher.txt
inst/extdata/demo/proteinpaint/heatmap_sample_group.txt
inst/extdata/demo/proteinpaint/heatmap_meta_template.txt
inst/extdata/demo/proteinpaint/heatmap_mutations.txt
vignettes/ngstk.Rmd man/get_files_ctime.Rd man/set_colors.Rd man/split_col_data.Rd man/muts2pp.Rd man/ngstk.Rd man/get_pp_samplegroup.Rd man/muts2oncoprinter.Rd man/format_pp_meta_gender.Rd man/split_row_data.Rd man/fusions2pp_meta.Rd man/show_mhanders.Rd man/format_pp_meta_age.Rd man/merge_table_files.Rd man/get_split_seqs.Rd man/format_pp_meta_fusions.Rd man/fusions2pp.Rd man/fusions2oncoprinter.Rd man/fusions_filter.Rd man/muts2mutation_mapper.Rd man/show_handers.Rd man/format_filenames.Rd man/split_list.Rd man/split_row_file.Rd man/set_tools.Rd man/get_files_mtime.Rd
build/vignette.rds
R/ngstk.R R/split.R R/merge.R R/proteinpaint_transefer.R R/filter.R R/cbioportal_trasefer.R R/hander.R R/format.R R/proteinpaint_utils.R R/log.R R/mhander.R R/utils.R tests/testthat.R tests/testthat/test_g_file.R tests/testthat/test_b_proteinpaint_transefer.R tests/testthat/test_e_hander.R tests/testthat/test_h_log.R tests/testthat/test_k_split.R tests/testthat/test_c_proteinpaint_utils.R tests/testthat/test_l_format.R tests/testthat/test_a_utils.R tests/testthat/test_d_filter.R tests/testthat/test_f_cbioportal_transefer.R
ngstk documentation built on Nov. 27, 2017, 5:03 p.m.