RiboProfiling

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see RiboProfiling.

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

Bioconductor version: 3.20

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 "4.4") 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")

Analysing Ribo-Seq data with the "RiboProfiling" package PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, PrincipalComponent, QualityControl, RiboSeq, Sequencing, Software

Version 1.36.0

In Bioconductor since BioC 3.2 (R-3.2) (9.5 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

System Requirements

URL

Suggests knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment

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Package Archives

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

Source Package RiboProfiling_1.36.0.tar.gz

Windows Binary (x86_64) RiboProfiling_1.36.0.zip

macOS Binary (x86_64) RiboProfiling_1.36.0.tgz

macOS Binary (arm64) RiboProfiling_1.36.0.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/

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