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
