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("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 | 1.0.0 |
| 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 | |
| Imports Me | |
| 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_1.0.0.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 |