calm

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see calm.

Covariate Assisted Large-scale Multiple testing


Bioconductor version: 3.14

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 "4.1") 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 1.8.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL (>=2)
Depends
Imports mgcv, stats, graphics
System Requirements
URL
Bug Reports https://github.com/k22liang/calm/issues
See More
Suggests knitr, rmarkdown
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 calm_1.8.0.tar.gz
Windows Binary calm_1.8.0.zip
macOS 10.13 (High Sierra) calm_1.8.0.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
Old Source Packages for BioC 3.14 Source Archive