DOTSeq
This is the released version of DOTSeq; for the devel version, see DOTSeq.
Genome-wide Detection of Differential ORF Usage
Bioconductor version: Release (3.23)
Differential open reading frame (ORF) translation analysis framework for ribosome profiling (Ribo-seq) with matched RNA-seq. Implements (i) Differential ORF Usage (DOU), a beta-binomial generalized linear model that models the expected proportion of Ribo-seq versus RNA-seq reads mapping to each ORF within a gene, and (ii) ORF-level Differential Translation Efficiency (DTE), a negative binomial GLM that capture changes in translation efficiency of individual ORFs across experimental conditions. Supports ORF-level read summarization for bulk and single-cell Ribo-seq.
Author: Chun Shen Lim [aut, cre]
, Gabrielle Chieng [aut, ctb]
, Marsden [fnd]
Maintainer: Chun Shen Lim <lim.bioinfo at gmail.com>
citation("DOTSeq")):
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")
BiocManager::install("DOTSeq")
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("DOTSeq")| DOTSeq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, DifferentialExpression, GeneExpression, GeneRegulation, Genetics, MultipleComparison, RNASeq, Regression, RiboSeq, Sequencing, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | ashr, boot, data.table, emmeans, glmmTMB, Matrix, methods, Rcpp, stats, utils, graphics, grDevices, pbapply, AnnotationDbi, BiocGenerics, BiocParallel, Biostrings, BSgenome, txdbmaker, DESeq2, GenomicAlignments, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, IRanges, rtracklayer, Rsamtools, S4Vectors, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/compgenom/DOTSeq |
| Bug Reports | https://github.com/compgenom/DOTSeq/issues |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, org.Hs.eg.db, curl, pasillaBamSubset, BiocStyle, biomaRt, DHARMa, eulerr, ggplot2, ggsignif, knitr, rmarkdown, testthat, withr, magick |
| Linking To | Rcpp |
| 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 | DOTSeq_1.0.0.tar.gz |
| Windows Binary (x86_64) | DOTSeq_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | DOTSeq_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | DOTSeq_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DOTSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DOTSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/DOTSeq/ |
| Package Short Url | https://bioconductor.org/packages/DOTSeq/ |
| Package Downloads Report | Download Stats |