topconfects

DOI: 10.18129/B9.bioc.topconfects  

Top Confident Effect Sizes

Bioconductor version: Release (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 monash.edu>

Installation

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

 

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

Details

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
LinkingTo
Suggests	limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/pfh/topconfects
BugReports	https://github.com/pfh/topconfects/issues
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	topconfects_1.14.0.zip
macOS Binary (x86_64)	topconfects_1.14.0.tgz
macOS Binary (arm64)	topconfects_1.14.0.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