To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RiboProfiling")

In most cases, you don't need to download the package archive at all.

RiboProfiling

DOI: 10.18129/B9.bioc.RiboProfiling    

This is the development version of RiboProfiling; for the stable release version, see RiboProfiling.

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

Bioconductor version: Development (3.6)

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>

Citation (from within R, enter citation("RiboProfiling")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RiboProfiling")

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 1.7.1
In Bioconductor since BioC 3.2 (R-3.2) (2 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
Build Report  

Package Archives

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

Source Package RiboProfiling_1.7.1.tar.gz
Windows Binary RiboProfiling_1.7.1.zip
Mac OS X 10.11 (El Capitan) RiboProfiling_1.7.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/RiboProfiling
Package Short Url http://bioconductor.org/packages/RiboProfiling/
Package Downloads Report Download Stats

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