Files in bedapub/ribiosExpression
Expression analysis component of ribios

.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/import.R R/io_gct_cls.R R/io_gmt.R R/io_tab.R R/mergeEset.R R/obsolete.R R/readAnnotationFile.R R/readFKtable.R R/ribiosExpression-package.R R/sniffFeatureType.R R/splitPCA.R R/summarizeProbesets.R R/summarizeSamples.R R/transformations.R R/truncateDgeTable.R README.md
data/ribios.ExpressionSet.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/ChipFetcher2ExpressionSet.Rd man/DesignContrast-class.Rd man/DesignContrast.Rd man/annotate-character-character-logical-method.Rd man/annotate-character-character-missing-method.Rd man/annotate-eSet-character-logical-method.Rd man/annotate-eSet-character-missing-method.Rd man/annotate.Rd man/assertFullRank.Rd man/contrastMatrix.Rd man/contrastNames.Rd man/contrastSampleIndices.Rd man/dataFrameTwoVecs.Rd man/design2group.Rd man/designMatrix.Rd man/designVariables.Rd man/dispGroups.Rd man/eSetToLongTable.Rd man/exprsToLong.Rd man/fixEmptyColumnName.Rd man/formatGmt.Rd man/groups.Rd man/grp2gmt.Rd man/isInputDesignConsistent.Rd man/keepMaxStatProbe.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/readAnnotationFile.Rd man/readEset.Rd man/readExprsMatrix.Rd man/readFKtable.Rd man/readFeatureAnnotationFile.Rd man/readGctCls.Rd man/readSampleAnnotationFile.Rd man/reannotate.Rd man/removeColRank.Rd man/ribios.ExpressionSet.Rd man/ribiosExpression-package.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
ribiosExpression.Rproj
tests/testthat.R tests/testthat/io_eset.R tests/testthat/test-DesignContrast.R tests/testthat/test-readFeatureAnnotationFile.R tests/testthat/test-readSampleAnnotationFile.R tests/testthat/test_gsea.R
bedapub/ribiosExpression documentation built on July 22, 2020, 4:07 p.m.