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

## Documentation for package ‘RiboProfiling’ version 1.6.0

- 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.