├── .Rbuildignore ├── .github └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── AllGenerics-definitions.R ├── AllGenerics.R ├── FRASER-package.R ├── Fraser-pipeline.R ├── FraserDataSet-class.R ├── RcppExports.R ├── annotationOfRanges.R ├── autoencoder.R ├── beta-binomial-testing.R ├── calculatePSIValue.R ├── countRNAseqData.R ├── example_functions.R ├── filterExpression.R ├── find_encoding_dimensions.R ├── fitCorrectionMethods.R ├── getNSetterFuns.R ├── getURLs.R ├── helper-functions.R ├── makeSimulatedDataset.R ├── mergeExternalData.R ├── plotMethods.R ├── pvalsNzscore.R ├── resultAnnotations.R ├── saveHDF5Objects.R ├── updateD.R ├── updateE.R ├── updateRho.R ├── variables.R └── zzz.R ├── README.md ├── codecov.yml ├── inst ├── CITATION └── extdata │ ├── README.md │ ├── bam │ ├── sample1.bam │ ├── sample1.bam.bai │ ├── sample2.bam │ ├── sample2.bam.bai │ ├── sample3.bam │ └── sample3.bam.bai │ ├── blacklist_regions │ ├── hg19-blacklist.v2.bed.gz │ └── hg38-blacklist.v2.bed.gz │ ├── externalCounts │ ├── annotation.tsv.gz │ ├── k_j_counts.tsv.gz │ ├── k_theta_counts.tsv.gz │ ├── n_psi3_counts.tsv.gz │ ├── n_psi5_counts.tsv.gz │ └── n_theta_counts.tsv.gz │ ├── raw_junction_counts.tsv.gz │ ├── raw_site_counts.tsv.gz │ ├── sampleTable.tsv │ ├── sampleTable_countTable.tsv │ └── seqLevels_dict │ ├── hg19_NCBI2UCSC.tsv │ └── hg38_NCBI2UCSC.tsv ├── man ├── FRASER.Rd ├── FraserDataSet-class.Rd ├── FraserDataSet.Rd ├── annotateRanges.Rd ├── assayNames-FraserDataSet-method.Rd ├── assays-FraserDataSet-method.Rd ├── calculatePSIValues.Rd ├── countRNA.Rd ├── counts.Rd ├── createTestFraserDataSet.Rd ├── estimateBestQ.Rd ├── fds-methods.Rd ├── filtering.Rd ├── fit.Rd ├── getter_setter_functions.Rd ├── injectOutliers.Rd ├── length-FraserDataSet-method.Rd ├── loadFraserDataSet.Rd ├── makeSimulatedFraserDataSet.Rd ├── mergeExternalData.Rd ├── plotFunctions.Rd ├── potentialImpactAnnotations.Rd ├── psiTypes.Rd ├── results.Rd └── subset.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp └── loss_n_gradient_functions.cpp ├── tests ├── testthat.R └── testthat │ ├── gradient_loss_R.R │ ├── helper.R │ ├── helper_test_data.R │ ├── test_annotation_methods.R │ ├── test_betabinom.R │ ├── test_counting.R │ ├── test_estimateBestQ.R │ ├── test_fraser_pipeline.R │ ├── test_getter_setter.R │ ├── test_plotJunctionDist.R │ ├── test_plotSampleResults.R │ ├── test_stats.R │ ├── test_updateSeqlevelsStyle.R │ ├── test_utils.R │ └── test_write_read_objects.R └── vignettes ├── FRASER.Rnw ├── FRASER_sketch.png ├── IntronJaccardIndex_sketch.png └── bibliography.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gagneurlab/FRASER/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/workflows/check-bioc.yml: 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