ribosomeProfilingQC

DOI: 10.18129/B9.bioc.ribosomeProfilingQC    

Ribosome Profiling Quality Control

Bioconductor version: Release (3.11)

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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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 1.0.6
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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
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_1.0.6.tar.gz
Windows Binary ribosomeProfilingQC_1.0.6.zip
macOS 10.13 (High Sierra) ribosomeProfilingQC_1.0.6.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
Old Source Packages for BioC 3.11 Source Archive

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