calm

DOI: 10.18129/B9.bioc.calm    

Covariate Assisted Large-scale Multiple testing

Bioconductor version: Release (3.10)

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 "3.6") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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_1.0.0.tar.gz
Windows Binary calm_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) calm_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/calm
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/calm
Package Short Url https://bioconductor.org/packages/calm/
Package Downloads Report Download Stats

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