Package: ODER
Title: Optimising the Definition of Expressed Regions
Version: 1.6.0
Date: 2021-04-13
Authors@R: 
    c(person(given = "Emmanuel",family = "Olagbaju",
           role = c("aut"),
           email = "eoolagbaju@gmail.com"),
           person(given = "David",family = "Zhang",
           role = c("aut", "cre"),
           email = "david.zhang.12@ucl.ac.uk",
           comment = c(ORCID = "0000-0003-2382-8460")),
           person(given = "Sebastian",family = "Guelfi",
           role = c("ctb"),
           email = "sebastian@vergegenomics.com"),
           person(given = "Siddharth",family = "Sethi",
           role = c("ctb"),
           email = "siddharth.sethi@astx.com"))
Description: 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. 
License: Artistic-2.0
URL: https://github.com/eolagbaju/ODER
BugReports: https://support.bioconductor.org/t/ODER
biocViews: Software, GenomeAnnotation, Transcriptomics, RNASeq,
        GeneExpression, Sequencing, DataImport
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Suggests: BiocStyle, covr, knitr, recount, RefManageR, rmarkdown,
        sessioninfo, SummarizedExperiment, testthat (>= 3.0.0),
        GenomicFeatures, xfun
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
Imports: BiocGenerics, BiocFileCache, dasper, derfinder, dplyr,
        IRanges, GenomeInfoDb, GenomicRanges, ggplot2, ggpubr, ggrepel,
        magrittr, rtracklayer, S4Vectors, stringr, data.table,
        megadepth, methods, plyr, purrr, tibble, utils
Depends: R (>= 4.1)
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/ODER
git_branch: RELEASE_3_17
git_last_commit: bba2c50
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: no
Packaged: 2023-04-25 22:00:23 UTC; biocbuild
Author: Emmanuel Olagbaju [aut],
  David Zhang [aut, cre] (<https://orcid.org/0000-0003-2382-8460>),
  Sebastian Guelfi [ctb],
  Siddharth Sethi [ctb]
Maintainer: David Zhang <david.zhang.12@ucl.ac.uk>
Built: R 4.6.1; ; 2026-08-13 14:18:01 UTC; unix
