Package: riboSeqR 1.47.0

Samuel Granjeaud

riboSeqR: Analysis of sequencing data from ribosome profiling experiments

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

Authors:Thomas J. Hardcastle [aut], Samuel Granjeaud [cre]

# Install 'riboSeqR' in R:

install.packages('riboSeqR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:riboSeqR-1.47.0(bioc 3.24)riboSeqR-1.46.0(bioc 3.23)

Last updated from:5bb214ae48. Checks:1 FAILURE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	FAILURE	164
linux-devel	OK	296
source / vignettes	OK	290
linux-release	OK	418
macos-release	OK	152
macos-oldrel	OK	143
windows-devel	OK	166
windows-release	OK	153
windows-oldrel	OK	157
wasm-release	OK	141

Last update: 2016-10-28
Started: 2014-09-24

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