topconfects
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see topconfects.
Top Confident Effect Sizes
Bioconductor version: 3.10
Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is 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>
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, MultipleComparison, RNASeq, Regression, Software, Transcriptomics, mRNAMicroarray |
| Version | 1.2.0 |
| 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 | |
| Imports Me | MetaVolcanoR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | topconfects_1.2.0.tar.gz |
| Windows Binary | topconfects_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | topconfects_1.2.0.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 3.10 | Source Archive |