RiboProfiling

DOI: 10.18129/B9.bioc.RiboProfiling    

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

Bioconductor version: Release (3.14)

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.

Author: Alexandra Popa

Maintainer: A. Popa <alexandra.mariela.popa at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RiboProfiling")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RiboProfiling")

 

PDF	R Script	Analysing Ribo-Seq data with the "RiboProfiling" package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Coverage, PrincipalComponent, QualityControl, RiboSeq, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 3.2 (R-3.2) (6.5 years)
License	GPL-3
Depends	R (>= 3.2.2), Biostrings
Imports	BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf
LinkingTo
Suggests	knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RiboProfiling_1.24.0.tar.gz
Windows Binary	RiboProfiling_1.24.0.zip (64-bit only)
macOS 10.13 (High Sierra)	RiboProfiling_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RiboProfiling
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RiboProfiling
Package Short Url	https://bioconductor.org/packages/RiboProfiling/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive