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>
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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, GenomeAnnotation, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2.5 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 |
| System Requirements | |
| URL | https://github.com/eolagbaju/ODER |
| Bug Reports | https://support.bioconductor.org/t/ODER |
See More
| Suggests | BiocStyle, covr, knitr, recount, RefManageR, rmarkdown, sessioninfo, SummarizedExperiment, testthat (>= 3.0.0), GenomicFeatures, xfun |
| Linking To | |
| 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 | 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 |
| Old Source Packages for BioC 3.17 | Source Archive |