API for genomation
Summary, annotation and visualization of genomic data

Global functions
AnnotationByFeature-class Man page
AnnotationByGeneParts-class Man page
AnnotationByGeneParts-method Man page
Max_c Man page Source code
Mean_c Man page Source code
Median_c Man page Source code
Min_c Man page Source code
Ops,ScoreMatrix,ScoreMatrix-method Man page
Ops,ScoreMatrixList,ScoreMatrixList-method Man page
Ops,ScoreMatrixList,numeric-method Man page
Ops,numeric,ScoreMatrixList-method Man page
RandomEnrichment-class Man page
ScoreMatrix Man page
ScoreMatrix,GRanges,GRanges-method Man page
ScoreMatrix,RleList,GRanges-method Man page
ScoreMatrix,character,GRanges-method Man page
ScoreMatrix-class Man page
ScoreMatrixBin Man page
ScoreMatrixBin,GRanges,GRanges-method Man page
ScoreMatrixBin,GRanges,GRangesList-method Man page
ScoreMatrixBin,RleList,GRanges-method Man page
ScoreMatrixBin,RleList,GRangesList-method Man page
ScoreMatrixBin,character,GRanges-method Man page
ScoreMatrixBin,character,GRangesList-method Man page
ScoreMatrixList Man page Source code
ScoreMatrixList-class Man page
Sum_c Man page Source code
[,ScoreMatrix,ANY,ANY,ANY-method Man page
[,ScoreMatrix-method Man page
[,ScoreMatrixList,ANY,ANY,ANY-method Man page
[,ScoreMatrixList-method Man page
annotatGrWithGeneParts Man page Source code
annotateWithFeature Man page
annotateWithFeature,GRanges,GRanges-method Man page
annotateWithFeatureFlank Man page
annotateWithFeatureFlank,GRanges,GRanges,GRanges-method Man page
annotateWithFeatures Man page
annotateWithFeatures,GRanges,GRangesList-method Man page
annotateWithFeatures,GRangesList,GRangesList-method Man page
annotateWithGeneParts Man page
annotateWithGeneParts,GRanges,GRangesList-method Man page
annotateWithGeneParts,GRangesList,GRangesList-method Man page
bed12ToExons Man page Source code
bed12ToIntrons Man page Source code
binMatrix Man page
binMatrix,ScoreMatrix-method Man page
binMatrix,ScoreMatrixList-method Man page
binMax Man page Source code
binMean Man page Source code
binMedian Man page Source code
binMin Man page Source code
binSum Man page Source code
binner Man page Source code
c.ScoreMatrix Man page Source code
c.ScoreMatrixList Man page Source code
cage Man page
calculateOverlapSignificance Man page
calculateOverlapSignificance,GRanges,GRanges-method Man page
checkBedValidity Man page Source code
checkClass Man page Source code
compressedAndUrl2temp Man page Source code
constrainRanges Man page Source code
convertBed2Exons Man page
convertBed2Exons,data.frame-method Man page
convertBed2Introns Man page
convertBed2Introns,data.frame-method Man page
convertBedDf Man page
convertBedDf,data.frame-method Man page
convertToColors Source code
cpgi Man page
detectUCSCheader Man page Source code
dispersion2 Source code
distance2NearestFeature Man page Source code
enrichmentMatrix Man page
enrichmentMatrix,ScoreMatrix,ScoreMatrix-method Man page
enrichmentMatrix,ScoreMatrixList,ScoreMatrix-method Man page
enrichmentMatrix,ScoreMatrixList,ScoreMatrixList-method Man page
file.ext Man page Source code
findFeatureComb Man page
findFeatureComb,GRangesList-method Man page
galpTo2Ranges Man page Source code
genes Man page
getAssociationWithTSS Man page
getAssociationWithTSS, Man page
getAssociationWithTSS,-methods Man page
getAssociationWithTSS,AnnotationByGeneParts-method Man page
getColors Man page Source code
getFeatsWithTargetsStats Man page
getFeatsWithTargetsStats,AnnotationByFeature-method Man page
getFlanks Man page
getFlanks,GRanges-method Man page
getMembers Man page
getMembers,AnnotationByFeature-method Man page
getPatternOccurrenceList.wrapper Source code
getRandomEnrichment Man page
getRandomEnrichment,GRanges,GRanges-method Man page
getTargetAnnotationStats Man page
getTargetAnnotationStats,AnnotationByFeature-method Man page
gffToGRanges Man page Source code
gridHeat Source code
heatLegendX Source code
heatLegendY Source code
heatMatrix Man page Source code
heatMeta Man page Source code
heatTargetAnnotation Man page Source code
intersectScoreMatrixList Man page
intersectScoreMatrixList,ScoreMatrixList-method Man page
listSliceMax Man page Source code
listSliceMean Man page Source code
listSliceMedian Man page Source code
listSliceMin Man page Source code
listSliceSum Man page Source code
multiHeatMatrix Man page Source code
nearest.2bed Source code
onUnload Source code
orderBy Man page
orderBy,ScoreMatrixList-method Man page
patternMatrix Man page
patternMatrix,character,DNAStringSet,ANY-method Man page
patternMatrix,character,DNAStringSet-method Man page
patternMatrix,character,GRanges,BSgenome-method Man page
patternMatrix,list,DNAStringSet,ANY-method Man page
patternMatrix,list,DNAStringSet-method Man page
patternMatrix,list,GRanges,BSgenome-method Man page
patternMatrix,matrix,DNAStringSet,ANY-method Man page
patternMatrix,matrix,DNAStringSet-method Man page
patternMatrix,matrix,GRanges,BSgenome-method Man page
patternPWM_windowsDNAStringSet2matrix Source code
patterncharacter_windowsDNAStringSet2matrix Source code
plotGeneAnnotation Man page Source code
plotLab Source code
plotMeta Man page Source code
plotTargetAnnotation Man page
plotTargetAnnotation,AnnotationByFeature-method Man page
plotXYlab Source code
promoters Man page
randomizeFeature Man page
randomizeFeature,GRanges-method Man page
read.zip Man page Source code
readBam Man page Source code
readBed Man page Source code
readBigWig Man page Source code
readBroadPeak Man page Source code
readFeatureFlank Man page
readFeatureFlank,character-method Man page
readGeneric Man page Source code
readNarrowPeak Man page Source code
readTableFast Man page Source code
readTranscriptFeatures Man page
readTranscriptFeatures,character-method Man page
rowSideCol Source code
scaleScoreMatrix Man page
scaleScoreMatrix,ScoreMatrix-method Man page
scaleScoreMatrixList Man page
scaleScoreMatrixList,ScoreMatrixList-method Man page
scan.sequence.with.pwm Source code
show,AnnotationByFeature-method Man page
show,AnnotationByGeneParts-method Man page
show,RandomEnrichment-method Man page
show,ScoreMatrix-method Man page
show,ScoreMatrixList-method Man page
target.type Man page Source code
test Source code
valid.ScoreMatrixList Source code
winsorize Source code
genomation documentation built on Nov. 1, 2018, 2:12 a.m.