Analysis of sequencing data from ribosome profiling experiments

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Documentation for package ‘riboSeqR’ version 1.26.0

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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"