Files in FRASER

Find RAre Splicing Events in RNA-Seq Data

NEWS

README.md

NAMESPACE

DESCRIPTION

LICENSE

R/RcppExports.R R/countRNAseqData.R R/AllGenerics-definitions.R R/saveHDF5Objects.R R/updateRho.R R/makeSimulatedDataset.R R/AllGenerics.R R/calculatePSIValue.R R/filterExpression.R R/fitCorrectionMethods.R R/find_encoding_dimensions.R R/updateE.R R/beta-binomial-testing.R R/FRASER-package.R R/annotationOfRanges.R R/Fraser-pipeline.R R/getURLs.R R/variables.R R/autoencoder.R R/updateD.R R/helper-functions.R R/zzz.R R/mergeExternalData.R R/pvalsNzscore.R R/FraserDataSet-class.R R/plotMethods.R R/getNSetterFuns.R R/example_functions.R

src/Makevars.win

src/Makevars

src/RcppExports.cpp

src/loss_n_gradient_functions.cpp

inst/CITATION

inst/doc/FRASER.pdf

inst/doc/FRASER.Rnw

inst/doc/FRASER.R

inst/extdata/sampleTable.tsv

inst/extdata/README.md

inst/extdata/raw_site_counts.tsv.gz

inst/extdata/sampleTable_countTable.tsv

inst/extdata/raw_junction_counts.tsv.gz

inst/extdata/bam/sample3.bam.bai

inst/extdata/bam/sample1.bam

inst/extdata/bam/sample2.bam

inst/extdata/bam/sample3.bam

inst/extdata/bam/sample1.bam.bai

inst/extdata/bam/sample2.bam.bai

inst/extdata/externalCounts/n_psi5_counts.tsv.gz

inst/extdata/externalCounts/k_j_counts.tsv.gz

inst/extdata/externalCounts/n_psi3_counts.tsv.gz

inst/extdata/externalCounts/k_theta_counts.tsv.gz

inst/extdata/externalCounts/n_theta_counts.tsv.gz

inst/extdata/externalCounts/annotation.tsv.gz

build/vignette.rds

tests/testthat.R tests/testthat/test_stats.R tests/testthat/test_betabinom.R tests/testthat/test_plotSampleResults.R tests/testthat/helper_test_data.R tests/testthat/test_hyperParams.R tests/testthat/test_annotation_methods.R tests/testthat/test_counting.R tests/testthat/gradient_loss_R.R tests/testthat/test_write_read_objects.R tests/testthat/helper.R tests/testthat/test_utils.R tests/testthat/test_plotJunctionDist.R tests/testthat/test_fraser_pipeline.R tests/testthat/test_getter_setter.R

vignettes/bibliography.bib

vignettes/FRASER_sketch.png

vignettes/FRASER.Rnw

man/filtering.Rd man/counts.Rd man/fit.Rd man/loadFraserDataSet.Rd man/assays-FraserDataSet-method.Rd man/psiTypes.Rd man/annotateRanges.Rd man/fds-methods.Rd man/assayNames-FraserDataSet-method.Rd man/makeSimulatedFraserDataSet.Rd man/countRNA.Rd man/FraserDataSet-class.Rd man/calculatePSIValues.Rd man/length-FraserDataSet-method.Rd man/mergeExternalData.Rd man/injectOutliers.Rd man/plotFunctions.Rd man/createTestFraserDataSet.Rd man/FRASER.Rd man/results.Rd man/FraserDataSet.Rd man/getter_setter_functions.Rd man/optimHyperParams.Rd man/subset.Rd

FRASER documentation built on Feb. 3, 2021, 2:01 a.m.