Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

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Documentation for package ‘RiboProfiling’ version 1.35.0

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

Help Pages

RiboProfiling-package	RiboProfiling.
aroundPromoter	Returns the flank size around the TSS for the x % CDSs
cdsPosTransc	Per transcript relative position of start and end codons for dataset ctrlGAlignments
codonDataCtrl	Codon frequency and coverage in ORFs on chromosome 1, for dataset ctrlGAlignments
codonIndexCovCtrl	The read coverage for each codon in ORFs on chromosome 1, for dataset ctrlGAlignments
codonInfo	Associates the read counts on codons with the codon type for each ORF.
codonPCA	PCA graphs on codon coverage
countShiftReads	Apply an offset on the read start along the transcript and returns the coverage on the 5pUTR, CDS, 3pUTR, as well as a matrix of codon coverage per ORF.
countsPlot	Graphs of sample read counts (quality assesment)
ctrlGAlignments	Ribosome profiling data on chr1 in human primary BJ fibroblasts control data: PMID: 23594524.
histMatchLength	Histogram of match length distribution of reads.
orfRelativePos	Relative position of the start and stop codon along the transcript
plotSummarizedCov	Plots the summarized coverage in a specified range (e.g. around TSS) for the specified match sizes
printPCA	Plots the PCA scatterplots produced by codonPCA function.
readStartCov	Read start coverage around the TSS on the predifined CDSs
readsToStartOrEnd	Reads in GAlignments converted to either Read Start (5') or End (3') Positions
RiboProfiling	RiboProfiling.
riboSeqFromBAM	Starting from a BAM file path: quality plots, shift ribosome position, coverage on multiple transcript features and on codons.