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>

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


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