Files in genomation

Summary, annotation and visualization of genomic data

README.md

.Rinstignore

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

src/RcppExports.cpp

src/binSum.cpp

data/promoters.RData

data/genes.RData

data/cpgi.RData

data/cage.RData

R/patternMatrix.R R/plotMatrix.R R/Ops.R R/RcppExports.R R/deprecated_defunct.R R/enrichmentMatrix.R R/test_genomation_package.R R/scoreMatrixBin.R R/readAnnotate.R R/combineScoreMatrixList.R R/findFeatureComb.R R/scoreMatrixList.R R/readData.R R/documentData.R R/getRandomEnrichment.R R/scoreMatrix.R R/genomation-classes.R R/randomizeFeature.R

vignettes/GenomationManual-knitr.html

vignettes/GenomationManual.Rmd

vignettes/Figures/visualizeFeatureComb-1.png

vignettes/Figures/multiHeatMatrix1-1.png

vignettes/Figures/plotScaledProfile-1.png

vignettes/Figures/plotGeneAnnotation-2.png

vignettes/Figures/multiHeatMatrix2-1.png

vignettes/Figures/genomationFlowChart1.png

vignettes/Figures/heatMatrix2-1.png

vignettes/Figures/plotGeneAnnotation-1.png

vignettes/Figures/heatMatrix1-2.png

vignettes/Figures/ctcfScoreMatrixList-1.png

vignettes/Figures/heatMatrixScales-1.png

vignettes/Figures/heatMatrix1-1.png

man/show-methods.Rd man/distance2NearestFeature.Rd man/randomizeFeature-methods.Rd man/ScoreMatrixList-class.Rd man/detectUCSCheader.Rd man/binner.Rd man/Mean_c.Rd man/enrichmentMatrix-ScoreMatrixList-method.Rd man/c.ScoreMatrix.Rd man/binSum.Rd man/ScoreMatrix-class.Rd man/bed12ToExons.Rd man/enrichmentMatrix-ScoreMatrix-method.Rd man/findFeatureComb-methods.Rd man/RandomEnrichment-class.Rd man/binMin.Rd man/listSliceMedian.Rd man/readBroadPeak.Rd man/ScoreMatrix-methods.Rd man/getRandomEnrichment-methods.Rd man/Ops-numeric-ScoreMatrixList-method.Rd man/cpgi.Rd man/readNarrowPeak.Rd man/sub-ScoreMatrix-ANY-ANY-ANY-method.Rd man/getTargetAnnotationStats-methods.Rd man/Median_c.Rd man/checkClass.Rd man/Sum_c.Rd man/convertBed2Introns-methods.Rd man/Max_c.Rd man/Ops-ScoreMatrixList-numeric-method.Rd man/binMatrix-methods.Rd man/target.type.Rd man/convertBed2Exons-methods.Rd man/file.ext.Rd man/heatMatrix.Rd man/multiHeatMatrix.Rd man/compressedAndUrl2temp.Rd man/binMean.Rd man/intersectScoreMatrixList-methods.Rd man/orderBy-methods.Rd man/plotMeta.Rd man/enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method.Rd man/binMedian.Rd man/patternMatrix-methods.Rd man/annotateWithFeatures-methods.Rd man/calculateOverlapSignificance-methods.Rd man/listSliceMean.Rd man/getColors.Rd man/getFlanks-methods.Rd man/genes.Rd man/listSliceMin.Rd man/AnnotationByGeneParts-class.Rd man/Ops-ScoreMatrix-ScoreMatrix-method.Rd man/listSliceMax.Rd man/getFeatsWithTargetsStats-methods.Rd man/annotateWithGeneParts-methods.Rd man/readTableFast.Rd man/heatMeta.Rd man/annotateWithFeature-methods.Rd man/promoters.Rd man/checkBedValidity.Rd man/readBed.Rd man/ScoreMatrixList-methods.Rd man/scaleScoreMatrix-methods.Rd man/binMax.Rd man/Ops-ScoreMatrixList-ScoreMatrixList-method.Rd man/getMembers-methods.Rd man/scaleScoreMatrixList.Rd man/constrainRanges.Rd man/bed12ToIntrons.Rd man/c.ScoreMatrixList.Rd man/AnnotationByGeneParts-methods.Rd man/annotatGrWithGeneParts.Rd man/readTranscriptFeatures-methods.Rd man/read.zip.Rd man/annotateWithFeatureFlank-methods.Rd man/AnnotationByFeature-class.Rd man/readBigWig.Rd man/convertBedDf-methods.Rd man/plotTargetAnnotation-methods.Rd man/ScoreMatrixBin-methods.Rd man/gffToGRanges.Rd man/heatTargetAnnotation-methods.Rd man/Min_c.Rd man/readGeneric.Rd man/readBam.Rd man/listSliceSum.Rd man/readFeatureFlank-methods.Rd man/galpTo2Ranges.Rd man/cage.Rd man/sub-ScoreMatrixList-ANY-ANY-ANY-method.Rd tests/genomation_unit_tests.R

inst/genomation_logo.png

inst/CITATION

inst/doc/GenomationManual.R

inst/doc/GenomationManual.html

inst/doc/GenomationManual.Rmd

inst/extdata/ex.broadPeak

inst/extdata/tab3.bed

inst/extdata/tab2.bed

inst/extdata/EnhancersEncode.txt.Test

inst/extdata/ex.narrowPeak

inst/extdata/chr21.CpGi.hg19.bed

inst/extdata/chr21.refseq.hg19.gtf

inst/extdata/tab1.bed

inst/extdata/Fantom4.Cage.Test

inst/extdata/chr21.refseq.hg19.bed

inst/scripts/FunctionNames.txt

inst/scripts/produceDataForExamples.R inst/scripts/devtools_test.R

inst/unitTests/tab.test2

inst/unitTests/test_pairedend.bam

inst/unitTests/test_ScoreMatrixBin.R

inst/unitTests/test.gtf

inst/unitTests/test_ScoreMatrixList.R

inst/unitTests/test.bedGraph

inst/unitTests/test.bw

inst/unitTests/tab.test3

inst/unitTests/test.bam

inst/unitTests/test_PatternMatrix.R inst/unitTests/test_ScoreMatrix.R

inst/unitTests/tab.test3.zip

inst/unitTests/tab.test1

inst/unitTests/tab.test4

inst/unitTests/test_enrichmentMatrix.R

inst/unitTests/test.bam.bai

inst/unitTests/test_pairedend.bam.bai

inst/unitTests/test_readData.R

genomation documentation built on Nov. 8, 2020, 5:21 p.m.