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ribosomeProfilingQC

Ribosome Profiling Quality Control

Bioconductor version: 3.23 · Package version: 1.24.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ribosomeProfilingQC")

Details

MaintainerJianhong Ou <jou@morgridge.org>
AuthorJianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>), Mariah Hoye [aut]
LicenseGPL (>=3) + file LICENSE
Downloads rank336
Source branchRELEASE_3_23
biocViewsCoverage, GeneRegulation, QualityControl, RiboSeq, Sequencing, Software, Visualization

Documentation

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Dependencies

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

Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, GenomeInfoDbData, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase