topconfects

DOI: 10.18129/B9.bioc.topconfects    

This is the development version of topconfects; to use it, please install the devel version of Bioconductor.

Top Confident Effect Sizes

Bioconductor version: Development (3.10)

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 (!requireNamespace("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")

 

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 1.1.0
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_1.1.0.tar.gz
Windows Binary topconfects_1.1.0.zip
Mac OS X 10.11 (El Capitan) topconfects_1.1.0.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 http://bioconductor.org/packages/topconfects/
Package Downloads Report Download Stats

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