Bias-aware Peak Calling and Quantification for MeRIP-Seq


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Documentation for package ‘exomePeak2’ version 1.6.0

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call_peaks_with_GLM Statistical Inference with DESeq package based on the provided reads count for exomic bins.
estimateSeqDepth Method estimateSeqDepth
estimateSeqDepth-method Method estimateSeqDepth
estimateSeqDepth-methods Method estimateSeqDepth
exomePeak2 Peak Calling and Peak Statistics Quantification on MeRIP-seq Dataset.
exomePeak2Results Method exomePeak2Results
exomePeak2Results-method Method exomePeak2Results
exomePeak2Results-methods Method exomePeak2Results
exomePeak2Results<- Method exomePeak2Results
exomePeak2Results<--method Method exomePeak2Results
exomePeakCalling Method exomePeakCalling
exomePeakCalling-method Method exomePeakCalling
exomePeakCalling-methods Method exomePeakCalling
exonPlot plot the distribution for the length of the overlapped exons.
exportResults Method exportResults
exportResults-method Method exportResults
exportResults-methods Method exportResults
GCsizeFactors Method GCsizeFactors
GCsizeFactors-method Method GCsizeFactors
GCsizeFactors-methods Method GCsizeFactors
GCsizeFactors<- Method GCsizeFactors
GCsizeFactors<--method Method GCsizeFactors
glmDM Method glmDM
glmDM-method Method glmDM
glmDM-methods Method glmDM
glmM Method glmM
glmM-method Method glmM
glmM-methods Method glmM
LibraryType Method LibraryType
LibraryType-method Method LibraryType
LibraryType-methods Method LibraryType
MeripBamFileList Maintain and use BAM files in MeRIP-Seq experiment
MeripBamFileList-class Maintain and use BAM files in MeRIP-Seq experiment
normalizeGC Method normalizeGC
normalizeGC-method Method normalizeGC
normalizeGC-methods Method normalizeGC
Parameter Method Parameter
Parameter-method Method Parameter
Parameter-methods Method Parameter
plotExonLength Method plotExonLength
plotExonLength-method Method plotExonLength
plotExonLength-methods Method plotExonLength
plotLfcGC Method plotLfcGC
plotLfcGC-method Method plotLfcGC
plotLfcGC-methods Method plotLfcGC
plotReadsGC Method plotReadsGC
plotReadsGC-method Method plotReadsGC
plotReadsGC-methods Method plotReadsGC
plotSizeFactors Method plotSizeFactors
plotSizeFactors-method Method plotSizeFactors
plotSizeFactors-methods Method plotSizeFactors
quiet Silencing unwanted function output.
Results Method Results
Results-method Method Results
Results-methods Method Results
scanMeripBAM Organize the BAM Files Information of a MeRIP-seq Data Set.
SummarizedExomePeak SummarizedExomePeak
SummarizedExomePeak-class SummarizedExomePeak