# Bias-aware Peak Calling and Quantification for MeRIP-Seq

## Documentation for package ‘exomePeak2’ version 1.4.0

- 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