topconfects

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see topconfects.

Top Confident Effect Sizes


Bioconductor version: 3.9

Find the largest confident effect sizes from a large collection, while maintaining False Discovery Rate and False Coverage-statement Rate control. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change.

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 "3.6") 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 1.0.0
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
URL https://github.com/pfh/topconfects
Bug Reports https://github.com/pfh/topconfects/issues
See More
Suggests limma, edgeR, DESeq2, NBPSeq, dplyr, testthat, knitr, rmarkdown, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package topconfects_1.0.0.tar.gz
Windows Binary topconfects_1.0.0.zip
Mac OS X 10.11 (El Capitan) topconfects_1.0.0.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
Old Source Packages for BioC 3.9 Source Archive