Files in alexchwong/SpliceWiz
interactive analysis and visualization of alternative splicing in R
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/ASE-GLM-edgeR.R
R/ASE-methods.R
R/ASEFilter-methods.R
R/AllClasses.R
R/AllGenerics.R
R/AllImports.R
R/BuildRef.R
R/BuildRef_GO.R
R/CollateData.R
R/Coverage.R
R/File_finders.R
R/Filters.R
R/MakeSE.R
R/Mappability.R
R/NxtSE-methods.R
R/ProcessBAM.R
R/ProcessBAM_docs.R
R/RcppExports.R
R/STAR_utils.R
R/SpliceWiz-package.R
R/ViewRef.R
R/covDataObject-methods.R
R/covPlotObject-methods.R
R/covPlotly-methods.R
R/dash.R
R/dash_DE_server.R
R/dash_DE_ui.R
R/dash_GO_server.R
R/dash_GO_ui.R
R/dash_QC.R
R/dash_cov_server.R
R/dash_cov_ui.R
R/dash_expr_server.R
R/dash_expr_ui.R
R/dash_filterModules.R
R/dash_filters.R
R/dash_globals.R
R/dash_ref_new_server.R
R/dash_ref_new_ui.R
R/dash_server.R
R/dash_settings.R
R/dash_ui.R
R/dash_vis_server.R
R/dash_vis_ui.R
R/example_data.R
R/ggplot_themes.R
R/globals.R
R/make_plot_data.R
R/plotCoverage.R
R/utils.R
R/wrappers.R
R/zzz.R
README.md
cleanup
configure
configure.win
inst/CITATION
inst/extdata/02H003.cov
inst/extdata/02H025.cov
inst/extdata/02H026.cov
inst/extdata/02H033.cov
inst/extdata/02H043.cov
inst/extdata/02H046.cov
inst/extdata/example_NxtSE.Rds
inst/extdata/example_NxtSE_novel.Rds
inst/extdata/labLogo.jpg
inst/extdata/spoof_1.fq
inst/extdata/spoof_2.fq
inst/extra-input-files/Human_hg19_nonPolyA_ROI.bed
inst/extra-input-files/Human_hg38_nonPolyA_ROI.bed
inst/extra-input-files/Mouse_mm10_nonPolyA_ROI.bed
inst/extra-input-files/Mouse_mm9_nonPolyA_ROI.bed
inst/htslib_version/DESCRIPTION
inst/htslib_version/NAMESPACE
inst/htslib_version/R/ProcessBAM_hts.R
inst/htslib_version/README.md
inst/htslib_version/src/BAM2blocks_htslib.cpp
inst/htslib_version/src/BAM2blocks_htslib.h
inst/htslib_version/src/Makevars.in
inst/htslib_version/src/Makevars.win
inst/htslib_version/src/hts_main.cpp
inst/htslib_version/src/hts_main.h
inst/htslib_version/src/swEngine_hts.cpp
inst/htslib_version/src/swEngine_hts.h
inst/htslib_version/tests/testthat/test-OpenMP-hts.R
inst/htslib_version/tests/testthat/test-SpliceWiz-hts.R
inst/scripts/make-data.R
man/ASE-GLM-edgeR.Rd
man/ASE-methods.Rd
man/ASEFilter-class.Rd
man/Build-Reference-methods.Rd
man/Coverage.Rd
man/Gene-ontology-methods.Rd
man/Graphics-User-Interface.Rd
man/Mappability-methods.Rd
man/NxtSE-class.Rd
man/Run_SpliceWiz_Filters.Rd
man/STAR-methods.Rd
man/SpliceWiz-package.Rd
man/View-Reference-methods.Rd
man/collateData.Rd
man/coord2GR.Rd
man/covDataObject-class.Rd
man/covPlotObject-class.Rd
man/covPlotly-class.Rd
man/example-SpliceWiz-data.Rd
man/findSamples.Rd
man/isCOV.Rd
man/makeSE.Rd
man/make_plot_data.Rd
man/plotCoverage.Rd
man/processBAM.Rd
man/setSWthreads.Rd
man/theme_white.Rd
src/.gitignore
src/BAM2blocks.cpp
src/BAM2blocks.h
src/FastaReader.cpp
src/FastaReader.h
src/FragmentBlocks.cpp
src/FragmentBlocks.h
src/GZTools.cpp
src/GZTools.h
src/Makevars.in
src/Makevars.win
src/RcppExports.cpp
src/ReadBlockProcessor.cpp
src/ReadBlockProcessor.h
src/ReadBlockProcessor_CoverageBlocks.cpp
src/ReadBlockProcessor_CoverageBlocks.h
src/ReadBlockProcessor_FragmentsMap.cpp
src/ReadBlockProcessor_FragmentsMap.h
src/ReadBlockProcessor_TandemJunctions.cpp
src/ReadBlockProcessor_TandemJunctions.h
src/SpliceWiz.h
src/covTools.cpp
src/covTools.h
src/includedefine.h
src/main.cpp
src/main.h
src/swEngine.cpp
src/swEngine.h
src/synthReadGenerator.cpp
src/synthReadGenerator.h
tests/testthat.R
tests/testthat/test-Mappa.R
tests/testthat/test-OpenMP.R
tests/testthat/test-SpliceWiz-GTF.R
tests/testthat/test-SpliceWiz-Novel.R
tests/testthat/test-SpliceWiz.R
vignettes/SW_Cookbook.Rmd
vignettes/SW_QuickStart.Rmd
vignettes/img/DE_edgeR.jpg
vignettes/img/DE_empty.jpg
vignettes/img/Expr_anno_columns.jpg
vignettes/img/Expr_cd_settings.jpg
vignettes/img/Expr_drop_2.jpg
vignettes/img/Expr_empty.jpg
vignettes/img/Expr_import_anno.jpg
vignettes/img/Expr_load_empty.jpg
vignettes/img/Expr_load_folder.jpg
vignettes/img/Expr_pb.jpg
vignettes/img/Filters_applied.jpg
vignettes/img/Filters_empty.jpg
vignettes/img/MenuBar.jpg
vignettes/img/Vis_GO.jpg
vignettes/img/Vis_cov1.jpg
vignettes/img/Vis_cov2.jpg
vignettes/img/Vis_cov3.jpg
vignettes/img/Vis_heatmap.jpg
vignettes/img/Vis_scatter.jpg
vignettes/img/Vis_scatter_highlighted.jpg
vignettes/img/Vis_volcano.jpg
vignettes/img/Vis_volcano_select.jpg
vignettes/img/buildRef.jpg
