Files in gagneurlab/OUTRIDER

OUTRIDER - OUTlier in RNA-Seq fInDER

R/AllGenerics.R R/OUTRIDER.R R/PCAcorrections.R R/RcppExports.R R/ZscoreMatrix.R R/autoencoder.R R/class-OutriderDataSet.R R/controlForConfounders.R R/filterExpression.R R/fitNB.R R/getNSetterFuns.R R/getNSetterFunsInternal.R R/helperFunctions.R R/inputCheckerFunctions.R R/lossNGradientRVersion.R R/method-counts.R R/method-evaluation.R R/method-gridSearch.R R/method-plot.R R/method-results.R R/pValMatrix.R R/package-OUTRIDER.R R/sizeFactor.R R/thetaMethodOfMoments.R R/updateD.R R/updateE.R R/updateTheta.R README.md man/OUTRIDER.Rd man/OutriderDataSet-class.Rd man/aberrant.Rd man/computeGeneLength.Rd man/computeLatentSpace.Rd man/computePvalues.Rd man/computeZscores.Rd man/controlForConfounders.Rd man/counts.Rd man/estimateBestQ.Rd man/filterExpression.Rd man/findEncodingDim.Rd man/fit.Rd man/fpkm.Rd man/getter_setter_functions.Rd man/makeExampleOutriderDataSet.Rd man/normalizationFactors.Rd man/plotFunctions.Rd man/results.Rd man/sampleExclusionMask.Rd man/sizeFactors.Rd tests/testthat.R tests/testthat/helper_test_data_set.R tests/testthat/test_OUTRIDERMain.R tests/testthat/test_OutriderDataSet.R tests/testthat/test_Rautoenc_fit.R tests/testthat/test_Rautoenc_loss.R tests/testthat/test_against_old_version.R tests/testthat/test_filtering.R tests/testthat/test_findEncodingDim.R tests/testthat/test_generics.R tests/testthat/test_helper.R tests/testthat/test_methods.R tests/testthat/test_plotting.R vignettes/gradient.pdf