Files in gagneurlab/OUTRIDER
OUTRIDER - OUTlier in RNA-Seq fInDER
.Rbuildignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
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
codecov.yml
inst/CITATION
inst/extdata/GTExSkinSmall.tsv
inst/extdata/KremerNBaderSmall.tsv
inst/extdata/gencode.v19.genes.small.gtf.gz
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
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/loss_n_gradient_functions.cpp
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/OUTRIDER.Rnw
vignettes/autoencoder_sketch.png
vignettes/bibliography.bib
vignettes/gradient.pdf
vignettes/gradient.tex
