Analysis of sequencing data from ribosome profiling experiments

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Documentation for package ‘riboSeqR’ version 1.42.0

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

Help Pages

riboSeqR-package	Analysis of sequencing data from ribosome profiling experiments.
filterHits	Filters framecalled data based on the mean number of hits observed across a replicate group.
findCDS	Parses a transcriptome file looking for start/stop codons in frame.
frameCounting	Counts aligned reads within coding sequence regions by frame and footprint size, splitting by frame and footprint size.
lengthDist	A function plotting the density of lengths in a riboData object.
libScales	Generates library scaling factors from ribosome footprint (and associated RNA) data.
logoContext	Produces a motif of coding start context
plotCDS	Plots average ribosome footprint alignment to coding sequences at 5' and 3' ends.
plotFS	Analyses frame called ribosome footprint data within coding sequences and identifies likely frame-shift of different length ribosome footprint reads.
plotTranscript	Plots ribosome footprint abundance and mRNA coverage (if available) for a specific transcript.
readingFrame	Analyses frame called ribosome footprint data within coding sequences and identifies likely frame-shift of different length ribosome footprint reads.
readRibodata	Reads ribosomal and (optionally) rna data from alignment files.
riboCoding	Class "riboCoding"
riboCoding-class	Class "riboCoding"
riboData	Class "riboData"
riboData-class	Class "riboData"
riboSeqR	Analysis of sequencing data from ribosome profiling experiments.
rnaCounts	Extracts mRNA counts from a riboDat object for a set of coding sequence coordinates.
show-method	Class "riboCoding"
sliceCounts	Slices out count data from riboCoding object for use in differential translation analyses.
[-method	Class "riboCoding"