ODER

DOI: 10.18129/B9.bioc.ODER  

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

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ODER.

Optimising the Definition of Expressed Regions

Bioconductor version: 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>

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")

 

HTML	R Script	Introduction to ODER
PDF		Reference Manual
Text		NEWS

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
LinkingTo
Suggests	BiocStyle, covr, knitr, recount, RefManageR, rmarkdown, sessioninfo, SummarizedExperiment, testthat (>= 3.0.0), GenomicFeatures, xfun
SystemRequirements
Enhances
URL	https://github.com/eolagbaju/ODER
BugReports	https://support.bioconductor.org/t/ODER
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/
Package Downloads Report	Download Stats