# Ribosome Profiling Quality Control

## 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"'