Registration Open for Bioc2024 July 24-26


Top Confident Effect Sizes

Bioconductor version: Release (3.19)

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 "4.4") 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:

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


biocViews DifferentialExpression, GeneExpression, MultipleComparison, RNASeq, Regression, Software, Transcriptomics, mRNAMicroarray
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License LGPL-2.1 | file LICENSE
Depends R (>= 3.6.0)
Imports methods, utils, stats, assertthat, ggplot2
System Requirements
Bug Reports
See More
Suggests limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle
Linking To
Depends On Me
Imports Me GeoTcgaData, weitrix
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package topconfects_1.20.0.tar.gz
Windows Binary
macOS Binary (x86_64) topconfects_1.20.0.tgz
macOS Binary (arm64) topconfects_1.20.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats