ribosomeProfilingQC
Ribosome Profiling Quality Control
Bioconductor version: Release (3.20)
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("ribosomeProfilingQC")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Coverage, GeneRegulation, QualityControl, RiboSeq, Sequencing, Software, Visualization |
Version | 1.18.0 |
In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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, 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.
Source Package | ribosomeProfilingQC_1.18.0.tar.gz |
Windows Binary (x86_64) | ribosomeProfilingQC_1.18.0.zip (64-bit only) |
macOS Binary (x86_64) | ribosomeProfilingQC_1.18.0.tgz |
macOS Binary (arm64) | ribosomeProfilingQC_1.17.1.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/ |
Package Downloads Report | Download Stats |