ribosomeProfilingQC
This is the development version of ribosomeProfilingQC; for the stable release version, see ribosomeProfilingQC.
Ribosome Profiling Quality Control
Bioconductor version: Development (3.21)
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:
Maintainer: Jianhong Ou <jianhong.ou at duke.edu>
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")| ribosomeProfilingQC Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, GeneRegulation, QualityControl, RiboSeq, Sequencing, Software, Visualization |
| Version | 1.19.0 |
| 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_1.19.0.tar.gz |
| Windows Binary (x86_64) | ribosomeProfilingQC_1.19.0.zip (64-bit only) |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |