ribosomeProfilingQC

DOI: 10.18129/B9.bioc.ribosomeProfilingQC    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ribosomeProfilingQC.

Ribosome Profiling Quality Control

Bioconductor version: 3.14

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

Author: Jianhong Ou [aut, cre] , Mariah Hoye [aut]

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Installation

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

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

BiocManager::install("ribosomeProfilingQC")

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("ribosomeProfilingQC")

 

HTML	R Script	ribosomeProfilingQC Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Coverage, GeneRegulation, QualityControl, RiboSeq, Sequencing, Software, Visualization
Version	1.6.1
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
License	GPL (>=3) + file LICENSE
Depends	R (>= 4.0), GenomicRanges
Imports	AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid
LinkingTo
Suggests	RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat, rmarkdown
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	ribosomeProfilingQC_1.6.1.tar.gz
Windows Binary	ribosomeProfilingQC_1.6.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	ribosomeProfilingQC_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ribosomeProfilingQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ribosomeProfilingQC
Package Short Url	https://bioconductor.org/packages/ribosomeProfilingQC/
Package Downloads Report	Download Stats