topconfects

DOI: 10.18129/B9.bioc.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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	LGPL-2.1 | file LICENSE
Depends	R (>= 3.6.0)
Imports	methods, utils, stats, assertthat, ggplot2
LinkingTo
Suggests	limma, edgeR, DESeq2, NBPSeq, dplyr, testthat, knitr, rmarkdown, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi
SystemRequirements
Enhances
URL	https://github.com/pfh/topconfects
BugReports	https://github.com/pfh/topconfects/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
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
Package Short Url	https://bioconductor.org/packages/topconfects/
Package Downloads Report	Download Stats