ribosomeProfilingQC

DOI: 10.18129/B9.bioc.ribosomeProfilingQC    

This is the development version of ribosomeProfilingQC; for the stable release version, see ribosomeProfilingQC.

Ribosome Profiling Quality Control

Bioconductor version: Development (3.15)

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 <jianhong.ou at duke.edu>, Mariah Hoye <mariah.hoye at duke.edu>

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

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

Installation

To install this package, start R (version "4.2") and enter:

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

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

BiocManager::install("ribosomeProfilingQC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Coverage, GeneRegulation, QualityControl, RiboSeq, Sequencing, Software, Visualization
Version 1.7.0
In Bioconductor since BioC 3.11 (R-4.0) (1.5 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
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URL
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Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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/
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