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RiboProfiling (version 1.0.0)

Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

Description

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

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Version

Version

1.0.0

License

GPL-3

Maintainer

A Popa

Last Published

February 15th, 2017

Functions in RiboProfiling (1.0.0)

Returns the flank size around the TSS for the x % CDSs

Codon frequency and coverage in ORFs on chromosome 1, for dataset ctrlGAlignments

countShiftReads

Apply an offset on the read start along the transcript and returns the coverage on the 5pUTR, CDS, 3pUTR, as well as a matrix of codon coverage per ORF.

Associates the read counts on codons with the codon type for each ORF.

Graphs of sample read counts (quality assesment)

ctrlGAlignments

Ribosome profiling data on chr1 in human primary BJ fibroblasts control data: PMID: 23594524.

codonIndexCovCtrl

The read coverage for each codon in ORFs on chromosome 1, for dataset ctrlGAlignments

histMatchLength

Histogram of match length distribution of reads.

Relative position of the start and stop codon along the transcript

PCA graphs on codon coverage

Read start coverage around the TSS on the predifined CDSs

readsToReadStart

Transforms the reads in GAlignments to Read Start Positions in GRanges

plotSummarizedCov

Plots the summarized coverage in a specified range (e.g. around TSS) for the specified match sizes

Plots the PCA scatterplots produced by codonPCA function.

Starting from a BAM file path: quality plots, shift ribosome position, coverage on multiple transcript features and on codons.