Package: topconfects
Title: Top Confident Effect Sizes
Version: 1.25.0
Authors@R: person("Paul", "Harrison", email = "paul.harrison@monash.edu", role = c("aut", "cre"), comment=c(ORCID="0000-0002-3980-268X"))
Description: Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is an alternative presentation of TREAT results with improved usability, eliminating p-values and instead providing confidence bounds. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change, but it can be applied to any collection of effect sizes with associated standard errors.
Depends: R (>= 3.6.0)
Imports: methods, utils, stats, assertthat, ggplot2, scales, grid,
        grDevices
Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat,
        reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr,
        rmarkdown, BiocStyle
License: LGPL-2.1 | file LICENSE
URL: https://github.com/pfh/topconfects
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
BugReports: https://github.com/pfh/topconfects/issues
biocViews: GeneExpression, DifferentialExpression, Transcriptomics,
        RNASeq, mRNAMicroarray, Regression, MultipleComparison
git_url: https://git.bioconductor.org/packages/topconfects
git_branch: devel
git_last_commit: a132e8d
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 02:39:00 UTC; biocbuild
Author: Paul Harrison [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3980-268X>)
Maintainer: Paul Harrison <paul.harrison@monash.edu>
Built: R 4.5.0; ; 2025-06-05 14:14:03 UTC; windows
