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ribosomeProfilingQC

Ribosome Profiling Quality Control


Bioconductor version: Release (3.18)

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 "4.3") 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")
ribosomeProfilingQC Vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Coverage, GeneRegulation, QualityControl, RiboSeq, Sequencing, Software, Visualization
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements
URL
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Suggests RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat, rmarkdown
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Package Archives

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

Source Package ribosomeProfilingQC_1.14.0.tar.gz
Windows Binary ribosomeProfilingQC_1.14.0.zip
macOS Binary (x86_64) ribosomeProfilingQC_1.14.0.tgz
macOS Binary (arm64) ribosomeProfilingQC_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ribosomeProfilingQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ribosomeProfilingQC
Bioc Package Browser https://code.bioconductor.org/browse/ribosomeProfilingQC/
Package Short Url https://bioconductor.org/packages/ribosomeProfilingQC/
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