# Analysis of sequencing data from ribosome profiling experiments

## Documentation for package ‘riboSeqR’ version 1.40.0

- 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"