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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 (3.18)

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 (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, Coverage, PrincipalComponent, QualityControl, RiboSeq, Sequencing, Software
Version 1.31.0
In Bioconductor since BioC 3.2 (R-3.2) (8 years)
License GPL-3
Depends R (>= 3.5.0), Biostrings
Imports BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf
Linking To
Suggests knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment
System Requirements
Enhances
URL
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Package Archives

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

Source Package RiboProfiling_1.31.0.tar.gz
Windows Binary RiboProfiling_1.31.0.zip (64-bit only)
macOS Binary (x86_64) RiboProfiling_1.31.0.tgz
macOS Binary (arm64) RiboProfiling_1.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RiboProfiling
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RiboProfiling
Bioc Package Browser https://code.bioconductor.org/browse/RiboProfiling/
Package Short Url https://bioconductor.org/packages/RiboProfiling/
Package Downloads Report Download Stats