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Bioconductor - topconfects (development version)

topconfects

This is the development version of topconfects; for the stable release version, see topconfects.

Top Confident Effect Sizes

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-3980-268X

Maintainer: Paul Harrison <paul.harrison at monash.edu>

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews DifferentialExpression, GeneExpression, MultipleComparison, RNASeq, Regression, Software, Transcriptomics, mRNAMicroarray Version 1.25.0 In Bioconductor since BioC 3.9 (R-3.6) (6 years) License LGPL-2.1 | file LICENSE Depends R (>= 3.6.0) Imports methods, utils, stats, assertthat, ggplot2, scales, grid, grDevices System Requirements URL https://github.com/pfh/topconfects Bug Reports https://github.com/pfh/topconfects/issues See More Suggests limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle Linking To Enhances 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.

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