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topconfects

Top Confident Effect Sizes

Bioconductor version: Release (3.17)

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 monash.edu>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("topconfects")

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

Documentation

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

browseVignettes("topconfects")
An overview of topconfects HTML R Script
Confident fold change HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GeneExpression, MultipleComparison, RNASeq, Regression, Software, Transcriptomics, mRNAMicroarray
Version 1.16.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License LGPL-2.1 | file LICENSE
Depends R (>= 3.6.0)
Imports methods, utils, stats, assertthat, ggplot2
Linking To
Suggests limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle
System Requirements
Enhances
URL https://github.com/pfh/topconfects
Bug Reports https://github.com/pfh/topconfects/issues
See More
Depends On Me
Imports Me GeoTcgaData, 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_1.16.0.tar.gz
Windows Binary topconfects_1.16.0.zip
macOS Binary (x86_64) topconfects_1.16.0.tgz
macOS Binary (arm64) topconfects_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/topconfects
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/topconfects
Bioc Package Browser https://code.bioconductor.org/browse/topconfects/
Package Short Url https://bioconductor.org/packages/topconfects/
Package Downloads Report Download Stats