ribosomeProfilingQC

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Ribosome Profiling Quality Control

Bioconductor version: Development (3.24)

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

Maintainer: Jianhong Ou <jou at morgridge.org>

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

Jianhong Ou, Mariah Hoye. ribosomeProfilingQC: Ribosome Profiling Quality Control. doi:10.18129/B9.bioc.ribosomeProfilingQC, R package version 1.25.1, https://bioconductor.org/packages/ribosomeProfilingQC.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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 Guide	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	1.25.1
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	GPL (>=3) + file LICENSE
Depends	R (>= 4.0), GenomicRanges
Imports	AnnotationDbi, BiocGenerics, Biostrings, BSgenome, cigarillo, 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ribosomeProfilingQC_1.25.1.tar.gz
Windows Binary (x86_64)	ribosomeProfilingQC_1.25.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	ribosomeProfilingQC_1.25.1.tgz
macOS Binary (sonoma-arm64)	ribosomeProfilingQC_1.25.1.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