Man pages for ZhenWei10/exomePeak2
Peak calling and quantification for MeRIP-seq data sets.

call_peaks_with_GLMStatistical Inference with DESeq package based on the...
consDESeq2_DMCalculate the index for across sample differential...
consDESeq2_MCalculate the index for across sample modification...
convertTxDbConvert the txdb object into the full transcript and whole...
ctestExact poisson test on the ratio between IP and input counts.
decision_deseqCalculate the decision table for a DESeq result.
decision_deseq2Calculate the decision table for a DESeq2 result.
DESeq2ResultsAccessor to the slot 'DESeq2Results' in class...
disj_backgroundFind the background of the user provided mod_gration.
estimateSeqDepthEstimate the Sequencing Depth Size Factors for Peak...
exome_bins_from_txdbextract exome bins for peak calling given a txdb object
exomePeak2Peak Calling and Peak Statistics Quantification on MeRIP-seq...
exomePeakCallingPerform Peak Calling on MeRIP-seq Dataset.
ExonPlotplot the distribution for the length of the overlapped exons.
exons_by_unique_geneExtracting exons by the corresponding genes that are on the...
exportResultsExport the (Differential) Modification Peaks/Sites and their...
flank_on_exonsFlank ranges on exon coordinate.
GC_content_over_grlRetrieve GC content level from genome over regions defined by...
GCsizeFactorsAccessor to the slot 'GCsizeFactors' in class...
glmDMEstimation and Inference on RNA Differential Modification...
GLM_inferenceStatistical Inference with DESeq2 on IP over input fold...
glmMEstimation and Inference on IP/input Log2 Fold Changes with...
LibraryTypeAccessor to the slot 'LibraryType' in class...
mclust_bgFind background of merip-seq signal with model based...
MeripBamFileList-classMeripBamFileList
normalizeGCEstimate Normalization Factors for GC content Bias...
ParameterAccessor to the slot 'Parameter' in class 'MeripBamFileList'.
plotExonLengthPlot the Distribution of the Length of Exons Overlapped by...
plotGuitarPlot the distribution of the peaks/sites on travis...
plotLfcGCScatter plot between the GLM log2FC estimates and GC content.
plotReadsGCPlot the linear relationships between GC content and reads...
plotSizeFactorsplot the size factors using different strategies.
quietSilencing unwanted function output.
reads_five_POSextract reads five prime POS.
reads_five_POS_revextract reads five prime POS and reverse its strand.
reduce_peaksA function to reduce ranges between elements within a...
remove_intronsRemoving introns from a provided GRanges object.
replace_bgReplace the control regions with user provided background.
ResultsReport the (Differential) Modification Peaks/Sites and their...
scanMeripBAMOrganize the BAM Files Information of a MeRIP-seq Data Set.
split_by_namea function to split a GRanges into GRangesList by its names.
SummarizedExomePeakSummarizedExomePeak
visualize_gene_binsA convenient function to help you quickly visualize the exome...
ZhenWei10/exomePeak2 documentation built on July 31, 2019, 4:29 p.m.