ribosomeProfilingQC
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see ribosomeProfilingQC.
Ribosome Profiling Quality Control
Bioconductor version: 3.11
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 "4.0") 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 | 1.0.6 |
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 |
See More
Suggests | RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat |
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_1.0.6.tar.gz |
Windows Binary | ribosomeProfilingQC_1.0.6.zip |
macOS 10.13 (High Sierra) | ribosomeProfilingQC_1.0.6.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 |
Old Source Packages for BioC 3.11 | Source Archive |