ribosomeProfilingQC
This is the development version of ribosomeProfilingQC; for the stable release version, see ribosomeProfilingQC.
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]
, Mariah Hoye [aut]
Maintainer: Jianhong Ou <jou at morgridge.org>
citation("ribosomeProfilingQC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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.
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ribosomeProfilingQC/ |
| Package Short Url | https://bioconductor.org/packages/ribosomeProfilingQC/ |
| Package Downloads Report | Download Stats |