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ribosomeProfilingQC
This is thereleased version of ribosomeProfilingQC; for the devel version, seeribosomeProfilingQC.
Ribosome Profiling Quality Control
Bioconductor version: Release (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("ribosomeProfilingQC")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("ribosomeProfilingQC")For older versions of R, please refer to the appropriateBioconductor 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 | 1.22.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 years) |
| License | GPL (>=3) + fileLICENSE |
| Depends | R (>= 4.0),GenomicRanges |
| Imports | AnnotationDbi,BiocGenerics,Biostrings,BSgenome,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
FollowInstallation instructions to use this package in your R session.
| Source Package | ribosomeProfilingQC_1.22.0.tar.gz |
| Windows Binary (x86_64) | ribosomeProfilingQC_1.22.0.zip |
| macOS Binary (x86_64) | ribosomeProfilingQC_1.22.0.tgz |
| macOS Binary (arm64) | ribosomeProfilingQC_1.22.0.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 |