Files in alexchwong/NxtIRFcore

Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS

R/ASE-methods.R R/AllClasses.R R/AllGenerics.R R/AllImports.R R/BuildRef.R R/CollateData.R R/Coverage.R R/File_finders.R R/Filters.R R/IRFinder.R R/MakeSE.R R/Mappability.R R/NxtFilter-methods.R R/NxtIRFcore-package.R R/NxtSE-methods.R R/RcppExports.R R/STAR_utils.R R/example_data.R R/ggplot_themes.R R/globals.R R/make_plot_data.R R/utils.R R/wrappers.R README.md

cleanup

configure

configure.win

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/metadata.csv

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/scripts/make-data.R man/ASE-methods.Rd man/BuildReference.Rd man/CollateData.Rd man/CoordToGR.Rd man/Coverage.Rd man/Find_Samples.Rd man/IRFinder.Rd man/IsCOV.Rd man/MakeSE.Rd man/Mappability-methods.Rd man/NxtFilter-class.Rd man/NxtIRFcore-package.Rd man/NxtSE-class.Rd man/Plot_Coverage.Rd man/Run_NxtIRF_Filters.Rd man/STAR-methods.Rd man/example-NxtIRF-data.Rd man/make_plot_data.Rd man/theme_white.Rd

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/IRFinder.cpp

src/IRFinder.h

src/IRFinder_Rcpp.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/covTools.cpp

src/covTools.h

src/includedefine.h

src/ompBAM.hpp

src/pbam1_t.hpp

src/pbam1_t_constructors.hpp

src/pbam1_t_getters.hpp

src/pbam1_t_internals.hpp

src/pbam1_t_tag_getters.hpp

src/pbam_defs.hpp

src/pbam_in.hpp

src/pbam_in_IO.hpp

src/pbam_in_constructors.hpp

src/pbam_in_decompress.hpp

src/pbam_in_fillReads.hpp

src/pbam_in_internals.hpp

src/pbam_in_supplyRead.hpp

tests/testthat.R tests/testthat/test-NxtIRFcore.R tests/testthat/test-OpenMP.R vignettes/NxtIRF.Rmd

alexchwong/NxtIRFcore documentation built on Oct. 31, 2022, 9:14 a.m.