Files in bedapub/ribiosExpression
Expression Analysis with RibiosExpression
.Rbuildignore
.github/workflows/standard-ci-workflow.yml
.gitignore
DESCRIPTION
Makefile
NAMESPACE
NEWS
R/AllClasses.R
R/AllGenerics.R
R/AllMethods.R
R/DesignContrast.R
R/annotate.R
R/assertFullRank.R
R/filter.R
R/fixDesignMatrixColnames.R
R/import.R
R/io_gct_cls.R
R/io_gmt.R
R/io_tab.R
R/limmaDgeTable.R
R/mergeEset.R
R/obsolete.R
R/readAnnotationFile.R
R/readFKtable.R
R/removeAllZeroVar.R
R/ribiosExpression-package.R
R/ribiosExpressionSet.R
R/sniffFeatureType.R
R/splitPCA.R
R/summarizeProbesets.R
R/summarizeSamples.R
R/transformations.R
R/truncateDgeTable.R
R/writeVarMetadata.R
README.md
data/ribios.ExpressionSet.RData
data/ribiosExpressionSet.RData
inst/Rscript/comp_diff.Rscript
inst/Rscript/keepMaxMeanProbes.Rscript
inst/Rscript/limma2gsea.Rscript
inst/Rscript/test-keepMaxMeanProbes.bash
inst/Rscript/test-limma2gsea.bash
inst/extdata/example-contrastMatrix.txt
inst/extdata/example-designMatrix.txt
inst/extdata/example-expression.gct
inst/extdata/featureAnnotation/featureAnnotationFile-withRowNames.txt
inst/extdata/featureAnnotation/featureAnnotationFile-withRowNamesFeatureName.txt
inst/extdata/featureAnnotation/featureAnnotationFile-withoutRowNames.txt
inst/extdata/featureAnnotation/featureAnnotationFile-withoutRowNamesFeatureName.txt
inst/extdata/sampleAnnotation/sampleAnnotationFile-withRowNames.txt
inst/extdata/sampleAnnotation/sampleAnnotationFile-withRowNamesSampleName.txt
inst/extdata/sampleAnnotation/sampleAnnotationFile-withoutRowNames.txt
inst/extdata/sampleAnnotation/sampleAnnotationFile-withoutRowNamesSampleName.txt
inst/extdata/sample_eset_exprs.txt
inst/extdata/sample_eset_fdata.txt
inst/extdata/sample_eset_pdata.txt
inst/extdata/tags_down.grp
inst/extdata/tags_up.grp
inst/extdata/test-limma2gsea.txt
inst/extdata/test.add.fData.txt
inst/extdata/test.add.pData.txt
inst/extdata/test.chip
inst/extdata/test.cls
inst/extdata/test.gct
inst/extdata/testKeepMaxMeanProbes-chip.gct
inst/extdata/testKeepMaxMeanProbes.txt
man/DesignContrast-class.Rd
man/DesignContrast.Rd
man/annotate.Rd
man/assertFullRank.Rd
man/contrastAnnotation-set.Rd
man/contrastAnnotation.Rd
man/contrastMatrix-set.Rd
man/contrastMatrix.Rd
man/contrastNames.Rd
man/contrastSampleIndices.Rd
man/dataFrameTwoVecs.Rd
man/design2group.Rd
man/designMatrix-set.Rd
man/designMatrix.Rd
man/designVariables.Rd
man/dispGroups.Rd
man/eSetToLongTable.Rd
man/exprsToLong.Rd
man/fixDesignMatrixColnames.Rd
man/fixEmptyColumnName.Rd
man/formatGmt.Rd
man/groups.Rd
man/grp2gmt.Rd
man/isInputDesignConsistent.Rd
man/keepMaxStatProbe.Rd
man/limmaDgeTable.Rd
man/limmaTopTable2dgeTable.Rd
man/matrixToLongTable.Rd
man/mergeEset.Rd
man/nContrast.Rd
man/parseContrastStr.Rd
man/parseDesignContrast.Rd
man/parseDesignContrastFile.Rd
man/parseDesignContrastStr.Rd
man/plot.DesignContrast.Rd
man/readAnnotationFile.Rd
man/readEset.Rd
man/readExprsMatrix.Rd
man/readFKtable.Rd
man/readFeatureAnnotationFile.Rd
man/readGctCls.Rd
man/readSampleAnnotationFile.Rd
man/reannotate.Rd
man/removeAllZeroVar.Rd
man/removeColRank.Rd
man/ribios.ExpressionSet.Rd
man/ribiosExpression-package.Rd
man/ribiosExpressionSet.Rd
man/rowscale.ExpressionSet.Rd
man/sniffFeatureType.Rd
man/splitPCA.Rd
man/summarizeProbesets.Rd
man/summarizeSamples.Rd
man/truncateDgeTable.Rd
man/writeEset.Rd
man/writeGct.Rd
man/writeGctCls.Rd
man/writeSampleGroups.Rd
man/writeVarMetadata.Rd
ribiosExpression.Rproj
tests/testthat.R
tests/testthat/io_eset.R
tests/testthat/test-DesignContrast.R
tests/testthat/test-fixDesignMatrixColnames.R
tests/testthat/test-readFeatureAnnotationFile.R
tests/testthat/test-readSampleAnnotationFile.R
tests/testthat/test-removeAllZeroVar.R
