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omicwas: Cell-Type-Specific Association Testing in Bulk Omics Experiments

In bulk epigenome/transcriptome experiments, molecular expression is measured in a tissue, which is a mixture of multiple types of cells. This package tests association of a disease/phenotype with a molecular marker for each cell type. The proportion of cell types in each sample needs to be given as input. The package is applicable to epigenome-wide association study (EWAS) and differential gene expression analysis. Takeuchi and Kato (submitted) "omicwas: cell-type-specific epigenome-wide and transcriptome association study".

Version: 0.8.0
Depends: R (≥ 3.6.0)
Imports: broom, data.table, dplyr, ff, glmnet, magrittr, MASS, matrixStats, parallel, purrr, rlang, tidyr
Suggests: testthat, knitr, rmarkdown
Published: 2020-10-08
DOI: 10.32614/CRAN.package.omicwas
Author: Fumihiko Takeuchi ORCID iD [aut, cre]
Maintainer: Fumihiko Takeuchi <fumihiko at takeuchi.name>
BugReports: https://github.com/fumi-github/omicwas/issues
License: GPL-3
URL: https://github.com/fumi-github/omicwas
NeedsCompilation: no
Materials: README
In views: Omics
CRAN checks: omicwas results

Documentation:

Reference manual: omicwas.pdf
Vignettes: Introduction to omicwas

Downloads:

Package source: omicwas_0.8.0.tar.gz
Windows binaries: r-devel: omicwas_0.8.0.zip, r-release: omicwas_0.8.0.zip, r-oldrel: omicwas_0.8.0.zip
macOS binaries: r-release (arm64): omicwas_0.8.0.tgz, r-oldrel (arm64): omicwas_0.8.0.tgz, r-release (x86_64): omicwas_0.8.0.tgz, r-oldrel (x86_64): omicwas_0.8.0.tgz
Old sources: omicwas archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=omicwas to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.