RiboProfiling

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RiboProfiling.

All versions

3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

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

Bioconductor version: Release (3.23)

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")):

Alexandra Popa. RiboProfiling: Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation. doi:10.18129/B9.bioc.RiboProfiling, R package version 1.42.0, https://bioconductor.org/packages/RiboProfiling.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Coverage, PrincipalComponent, QualityControl, RiboSeq, Sequencing, Software
Version	1.42.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 years)
License	GPL-3
Depends	R (>= 3.5.0), Biostrings
Imports	methods, BiocGenerics, Seqinfo, 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
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