DOTSeq
This is the development version of DOTSeq; to use it, please install the devel version of Bioconductor.
Differential Analysis of Translation Efficiency and Usage of Open Reading Frames
Bioconductor version: Development (3.23)
Differential 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 open reading frame (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 0.99.6 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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, pasillaBamSubset, BiocStyle, biomaRt, DHARMa, eulerr, ggplot2, ggsignif, knitr, rmarkdown, testthat, withr |
| 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_0.99.6.tar.gz |
| Windows Binary (x86_64) | DOTSeq_0.99.4.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DOTSeq_0.99.4.tgz |
| macOS Binary (big-sur-arm64) | DOTSeq_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | DOTSeq_0.99.4.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 |