Bias-aware Peak Calling and Quantification for MeRIP-Seq

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Documentation for package ‘exomePeak2’ version 1.6.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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