calm
This is the released version of calm; for the devel version, see calm.
Covariate Assisted Large-scale Multiple testing
Bioconductor version: Release (3.23)
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("calm")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, GeneExpression, Genetics, ImmunoOncology, Metabolomics, Microarray, MultipleComparison, Proteomics, RNASeq, Regression, Sequencing, Software, Transcriptomics |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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_1.26.0.tar.gz |
| Windows Binary (x86_64) | calm_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | calm_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | calm_1.26.0.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 |