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riboSeqR (version 1.6.0)

Analysis of sequencing data from ribosome profiling experiments.

Description

Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.

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Version

Version

1.6.0

License

GPL-3

Maintainer

Thomas J Hardcastle

Last Published

February 15th, 2017

Functions in riboSeqR (1.6.0)

readRibodata

Reads ribosomal and (optionally) rna data from alignment files.
rnaCounts

Extracts mRNA counts from a riboDat object for a set of coding sequence coordinates.
plotTranscript

Plots ribosome footprint abundance and mRNA coverage (if available) for a specific transcript.
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.
riboData-class

Class "riboData"
frameCounting

Counts aligned reads within coding sequence regions by frame and footprint size, splitting by frame and footprint size.
riboSeqR-package

Analysis of sequencing data from ribosome profiling experiments.
readingFrame

Analyses frame called ribosome footprint data within coding sequences and identifies likely frame-shift of different length ribosome footprint reads.
riboCoding-class

Class "riboCoding"
plotCDS

Plots average ribosome footprint alignment to coding sequences at 5' and 3' ends.
sliceCounts

Slices out count data from riboCoding object for use in differential translation analyses.
lengthDist

A function plotting the density of lengths in a riboData object.