ODER

DOI: 10.18129/B9.bioc.ODER    

This is the development version of ODER; for the stable release version, see ODER.

Optimising the Definition of Expressed Regions

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

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