Analysis of sequencing data from ribosome profiling experiments.


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Documentation for package ‘riboSeqR’ version 1.2.0

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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.
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"