DOI: 10.18129/B9.bioc.topconfects  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see topconfects.

Top Confident Effect Sizes

Bioconductor version: 3.16

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.

Author: Paul Harrison [aut, cre]

Maintainer: Paul Harrison <paul.harrison at>

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


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script An overview of topconfects
HTML R Script Confident fold change
PDF   Reference Manual
Text   NEWS


biocViews DifferentialExpression, GeneExpression, MultipleComparison, RNASeq, Regression, Software, Transcriptomics, mRNAMicroarray
Version 1.14.0
In Bioconductor since BioC 3.9 (R-3.6) (4 years)
License LGPL-2.1 | file LICENSE
Depends R (>= 3.6.0)
Imports methods, utils, stats, assertthat, ggplot2
Suggests limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle
Depends On Me
Imports Me MetaVolcanoR, weitrix
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package topconfects_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) topconfects_1.14.0.tgz
macOS Binary (arm64) topconfects_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: