Ribosome Profiling Quality Control

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Documentation for package ‘ribosomeProfilingQC’ version 1.16.0

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

Help Pages

$-method	Class '"cvgd"'
$<--method	Class '"cvgd"'
assignReadingFrame	Assign reading frame
codonBias	Codon usage bias
codonUsage	Start or Stop codon usage
countReads	Extract counts for RPFs and RNAs
coverageDepth	Extract coverage depth for gene level or transcript level
coverageRates	Calculate coverage rate
cvgd	Class '"cvgd"'
cvgd-class	Class '"cvgd"'
estimatePsite	Estimate P site position
filterCDS	Filter CDS by size
FLOSS	Fragment Length Organization Similarity Score (FLOSS)
frameCounts	Extract counts for gene level or transcript level
getFPKM	Get FPKM values for counts
getORFscore	Calculate ORFscore
getPsiteCoordinates	Get P site coordinates
ggBar	barplot by ggplot2
metaPlot	Metagene analysis plot
normalizeTEbyLoess	Normalize the TE by Loess
normBy	Normalization by edgeR, DESeq2 or RUVSeq
normByRUVs	Normalization by RUVSeq
PAmotif	Metaplot of P site distribution
plotDistance2Codon	Metaplot of P site distribution
plotFrameDensity	Plot density for each reading frame
plotSpliceEvent	Plot splice event
plotTE	Plot translational efficiency
plotTranscript	Plot reads P site abundance for a specific transcript
prepareCDS	Prepare CDS
readsDistribution	Plot reads distribution in genomic elements
readsEndPlot	Plot start/stop windows
readsLenToKeep	Get reads length to keep by cutoff percentage
ribosomeReleaseScore	Ribosome Release Score (RRS)
shiftReadsByFrame	Shift reads by reading frame
show-method	Class '"cvgd"'
simulateRPF	Simulation function
spliceEvent	Get splicing events
strandPlot	Plot the distribution of reads in sense and antisense strand
summaryReadsLength	Summary the reads lengths
translationalEfficiency	Translational Efficiency
[[-method	Class '"cvgd"'
[[<--method	Class '"cvgd"'