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RiboProfiling (version 1.2.2)

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

1.2.2

License

GPL-3

Maintainer

A Popa

Last Published

February 15th, 2017

Functions in RiboProfiling (1.2.2)

plotSummarizedCov

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

ctrlGAlignments

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

Relative position of the start and stop codon along the transcript

Read start coverage around the TSS on the predifined CDSs

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

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

Plots the PCA scatterplots produced by codonPCA function.

readsToStartOrEnd

Reads in GAlignments converted to either Read Start (5') or End (3') Positions

histMatchLength

Histogram of match length distribution of reads.

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.

Graphs of sample read counts (quality assesment)

codonIndexCovCtrl

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

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

PCA graphs on codon coverage

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