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
| Maintainer | Jianhong Ou <jou@morgridge.org> |
| Author | Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>), Mariah Hoye [aut] |
| License | GPL (>=3) + file LICENSE |
| Downloads rank | 336 |
| Source branch | RELEASE_3_23 |
| biocViews | Coverage, 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