Files in c-mertes/FraseR
Find RAre Splicing Events in RNA-Seq Data
.Rbuildignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/AllGenerics-definitions.R
R/AllGenerics.R
R/FRASER-package.R
R/Fraser-pipeline.R
R/FraserDataSet-class.R
R/RcppExports.R
R/annotationOfRanges.R
R/autoencoder.R
R/beta-binomial-testing.R
R/calculatePSIValue.R
R/countRNAseqData.R
R/example_functions.R
R/filterExpression.R
R/find_encoding_dimensions.R
R/fitCorrectionMethods.R
R/getNSetterFuns.R
R/getURLs.R
R/helper-functions.R
R/makeSimulatedDataset.R
R/mergeExternalData.R
R/plotMethods.R
R/pvalsNzscore.R
R/resultAnnotations.R
R/saveHDF5Objects.R
R/updateD.R
R/updateE.R
R/updateRho.R
R/variables.R
R/zzz.R
README.md
codecov.yml
inst/CITATION
inst/extdata/README.md
inst/extdata/bam/sample1.bam
inst/extdata/bam/sample1.bam.bai
inst/extdata/bam/sample2.bam
inst/extdata/bam/sample2.bam.bai
inst/extdata/bam/sample3.bam
inst/extdata/bam/sample3.bam.bai
inst/extdata/blacklist_regions/hg19-blacklist.v2.bed.gz
inst/extdata/blacklist_regions/hg38-blacklist.v2.bed.gz
inst/extdata/externalCounts/annotation.tsv.gz
inst/extdata/externalCounts/k_j_counts.tsv.gz
inst/extdata/externalCounts/k_theta_counts.tsv.gz
inst/extdata/externalCounts/n_psi3_counts.tsv.gz
inst/extdata/externalCounts/n_psi5_counts.tsv.gz
inst/extdata/externalCounts/n_theta_counts.tsv.gz
inst/extdata/raw_junction_counts.tsv.gz
inst/extdata/raw_site_counts.tsv.gz
inst/extdata/sampleTable.tsv
inst/extdata/sampleTable_countTable.tsv
man/FRASER.Rd
man/FraserDataSet-class.Rd
man/FraserDataSet.Rd
man/annotateRanges.Rd
man/assayNames-FraserDataSet-method.Rd
man/assays-FraserDataSet-method.Rd
man/calculatePSIValues.Rd
man/countRNA.Rd
man/counts.Rd
man/createTestFraserDataSet.Rd
man/fds-methods.Rd
man/filtering.Rd
man/fit.Rd
man/getter_setter_functions.Rd
man/injectOutliers.Rd
man/length-FraserDataSet-method.Rd
man/loadFraserDataSet.Rd
man/makeSimulatedFraserDataSet.Rd
man/mergeExternalData.Rd
man/optimHyperParams.Rd
man/plotFunctions.Rd
man/potentialImpactAnnotations.Rd
man/psiTypes.Rd
man/results.Rd
man/subset.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/loss_n_gradient_functions.cpp
tests/testthat.R
tests/testthat/gradient_loss_R.R
tests/testthat/helper.R
tests/testthat/helper_test_data.R
tests/testthat/test_annotation_methods.R
tests/testthat/test_betabinom.R
tests/testthat/test_counting.R
tests/testthat/test_fraser_pipeline.R
tests/testthat/test_getter_setter.R
tests/testthat/test_hyperParams.R
tests/testthat/test_plotJunctionDist.R
tests/testthat/test_plotSampleResults.R
tests/testthat/test_stats.R
tests/testthat/test_utils.R
tests/testthat/test_write_read_objects.R
vignettes/FRASER.Rnw
vignettes/FRASER.pdf
vignettes/FRASER_sketch.png
vignettes/IntronJaccardIndex_sketch.png
vignettes/bibliography.bib
