calm

DOI: 10.18129/B9.bioc.calm  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see calm.

Covariate Assisted Large-scale Multiple testing

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Bayesian, DifferentialExpression, GeneExpression, Genetics, ImmunoOncology, Metabolomics, Microarray, MultipleComparison, Proteomics, RNASeq, Regression, Sequencing, Software, Transcriptomics
Version	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
License	GPL (>=2)
Depends
Imports	mgcv, stats, graphics
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/k22liang/calm/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	calm_1.12.0.tar.gz
Windows Binary	calm_1.12.0.zip
macOS Binary (x86_64)	calm_1.12.0.tgz
macOS Binary (arm64)	calm_1.12.0.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