ribosomeProfilingQC

This is the released version of ribosomeProfilingQC; for the devel version, see ribosomeProfilingQC.

Ribosome Profiling Quality Control

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DOI: 10.18129/B9.bioc.ribosomeProfilingQC

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-8652-2488 , Mariah Hoye [aut]

Maintainer: Jianhong Ou <jou at morgridge.org>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, GeneRegulation, QualityControl, RiboSeq, Sequencing, Software, Visualization

Version 1.22.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 years)

License GPL (>=3) + file LICENSE

Depends R (>= 4.0), GenomicRanges

Imports AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, Seqinfo, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid, txdbmaker, ggExtra

System Requirements

URL

Suggests RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, GenomeInfoDbData, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase

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Package Archives

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

Source Package ribosomeProfilingQC_1.22.0.tar.gz

Windows Binary (x86_64) ribosomeProfilingQC_1.22.0.zip

macOS Binary (x86_64) ribosomeProfilingQC_1.22.0.tgz

macOS Binary (arm64) ribosomeProfilingQC_1.22.0.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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