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calm

Covariate Assisted Large-scale Multiple testing

Bioconductor version: Release (3.17)

Statistical methods for multiple testing with covariate information. Traditional multiple testing methods only consider a list of test statistics, such as p-values. Our methods incorporate the auxiliary information, such as the lengths of gene coding regions or the minor allele frequencies of SNPs, to improve power.

Author: Kun Liang [aut, cre]

Maintainer: Kun Liang <kun.liang at uwaterloo.ca>

Citation (from within R, enter citation("calm")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("calm")

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("calm")
Userguide for calm package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, DifferentialExpression, GeneExpression, Genetics, ImmunoOncology, Metabolomics, Microarray, MultipleComparison, Proteomics, RNASeq, Regression, Sequencing, Software, Transcriptomics
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License GPL (>=2)
Depends
Imports mgcv, stats, graphics
Linking To
Suggests knitr, rmarkdown
System Requirements
Enhances
URL
Bug Reports https://github.com/k22liang/calm/issues
See More
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 calm_1.14.0.tar.gz
Windows Binary calm_1.14.0.zip
macOS Binary (x86_64) calm_1.14.0.tgz
macOS Binary (arm64) calm_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/calm
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/calm
Bioc Package Browser https://code.bioconductor.org/browse/calm/
Package Short Url https://bioconductor.org/packages/calm/
Package Downloads Report Download Stats