Man pages for ribosomeProfilingQC
Ribosome Profiling Quality Control

assignReadingFrameAssign reading frame
codonUsageStart or Stop codon usage
countReadsExtract counts for RPFs and RNAs
coverageDepthExtract coverage depth for gene level or transcript level
coverageRatesCalculate coverage rate
cvgd-classClass '"cvgd"'
estimatePsiteEstimate P site position
filterCDSFilter CDS by size
FLOSSFragment Length Organization Similarity Score (FLOSS)
frameCountsExtract counts for gene level or transcript level
getFPKMGet FPKM values for counts
getORFscoreCalculate ORFscore
getPsiteCoordinatesGet P site coordinates
ggBarbarplot by ggplot2
metaPlotMetagene analysis plot
normByRUVsNormalization by RUVSeq
PAmotifMetaplot of P site distribution
plotDistance2CodonMetaplot of P site distribution
plotFrameDensityPlot density for each reading frame
plotSpliceEventPlot splice event
plotTEPlot translational efficiency
plotTranscriptPlot reads P site abundance for a specific transcript
prepareCDSPrepare CDS
readsDistributionPlot reads distribution in genomic elements
readsEndPlotPlot start/stop windows
readsLenToKeepGet reads length to keep by cutoff percentage
ribosomeReleaseScoreRibosome Release Score (RRS)
shiftReadsByFrameShift reads by reading frame
simulateRPFSimulation function
spliceEventGet splicing events
strandPlotPlot the distribution of reads in sense and antisense strand
summaryReadsLengthSummary the reads lengths
translationalEfficiencyTranslational Efficiency
ribosomeProfilingQC documentation built on March 13, 2021, 2:01 a.m.