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Bioconductor - ribosomeProfilingQC (development version)

ribosomeProfilingQC

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

Ribosome Profiling Quality Control

Bioconductor version: Development (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: 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")

# 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ribosomeProfilingQC")
Details biocViews Coverage, GeneRegulation, QualityControl, RiboSeq, Sequencing, Software, Visualization Version 1.21.1 In Bioconductor since BioC 3.11 (R-4.0) (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, txdbmaker, ggExtra System Requirements URL See More 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 Package Archives

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

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