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: 0.7.0
Depends: R (≥ 3.6.0)
Imports: broom, data.table, dplyr, ff, glmnet, magrittr, MASS, matrixStats, parallel, PCDimension, rlang, sva, tidyr
Suggests: testthat, knitr, rmarkdown
Published: 2020-06-02
Author: Fumihiko Takeuchi ORCID iD [aut, cre]
Maintainer: Fumihiko Takeuchi <fumihiko at>
License: GPL-3
NeedsCompilation: no
Materials: README
CRAN checks: omicwas results


Reference manual: omicwas.pdf
Vignettes: Introduction to omicwas
Package source: omicwas_0.7.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release: omicwas_0.7.0.tgz, r-oldrel: omicwas_0.7.0.tgz
Old sources: omicwas archive


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