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ODER

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Optimising the Definition of Expressed Regions

Bioconductor version: Release (3.17)

The aim of ODER is to identify previously unannotated expressed regions (ERs) using RNA-sequencing data. For this purpose, ODER defines and optimises the definition of ERs, then connected these ERs to genes using junction data. In this way, ODER improves gene annotation. Gene annotation is a staple input of many bioinformatic pipelines and a more complete gene annotation can enable more accurate interpretation of disease associated variants.

Author: Emmanuel Olagbaju [aut], David Zhang [aut, cre] , Sebastian Guelfi [ctb], Siddharth Sethi [ctb]

Maintainer: David Zhang <david.zhang.12 at ucl.ac.uk>

Citation (from within R, enter citation("ODER")):

Installation

To install this package, start R (version "4.3") and enter: 

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

BiocManager::install("ODER")

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("ODER")
Introduction to ODER HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, GeneExpression, GenomeAnnotation, RNASeq, Sequencing, Software, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports BiocGenerics, BiocFileCache, dasper, derfinder, dplyr, IRanges, GenomeInfoDb, GenomicRanges, ggplot2, ggpubr, ggrepel, magrittr, rtracklayer, S4Vectors, stringr, data.table, megadepth, methods, plyr, purrr, tibble, utils
Linking To
Suggests BiocStyle, covr, knitr, recount, RefManageR, rmarkdown, sessioninfo, SummarizedExperiment, testthat (>= 3.0.0), GenomicFeatures, xfun
System Requirements
Enhances
URL https://github.com/eolagbaju/ODER
Bug Reports https://support.bioconductor.org/t/ODER
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ODER_1.6.0.tar.gz
Windows Binary ODER_1.6.0.zip
macOS Binary (x86_64) ODER_1.6.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/ODER
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ODER
Package Short Url https://bioconductor.org/packages/ODER/
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