Installation | Usage | Analyzing DNA methylation | Analyzing gene expression | Analyzing mQTL
Package: omicwas 0.8.0
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".
Authors:
omicwas_0.8.0.tar.gz
omicwas_0.8.0.zip(r-4.7-any)omicwas_0.8.0.zip(r-4.6-any)omicwas_0.8.0.zip(r-4.5-any)
omicwas_0.8.0.tgz(r-4.6-any)omicwas_0.8.0.tgz(r-4.5-any)
omicwas_0.8.0.tar.gz(r-4.7-any)omicwas_0.8.0.tar.gz(r-4.6-any)
omicwas_0.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
omicwas/json (API)
| # Install 'omicwas' in R: |
| install.packages('omicwas', repos = c('https://fumi-github.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fumi-github/omicwas/issues
Datasets:
- GSE42861small - Small Subset of GSE42861 Dataset From GEO
- GSE79262small - Small Subset of GSE79262 Dataset From GEO
- GTExsmall - Small Subset of GTEx Dataset
Last updated from:1852179a55. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 153 | ||
| source / vignettes | OK | 252 | ||
| linux-release | OK | 147 | ||
| macos-release | OK | 224 | ||
| macos-oldrel | OK | 222 | ||
| windows-devel | OK | 114 | ||
| windows-release | OK | 92 | ||
| windows-oldrel | OK | 93 | ||
| wasm-release | OK | 114 |
Exports:ctassocctcisQTLrrs.fit
Dependencies:backportsbitbroomclicodetoolscpp11data.tabledplyrffforeachgenericsglmnetglueiteratorslatticelifecyclemagrittrMASSMatrixmatrixStatspillarpkgconfigpurrrR6RcppRcppEigenrlangshapestringistringrsurvivaltibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cell-Type-Specific Association Testing | ctassoc |
| Cell-Type-Specific QTL analysis | ctcisQTL |
| Small Subset of GSE42861 Dataset From GEO | GSE42861small |
| Small Subset of GSE79262 Dataset From GEO | GSE79262small |
| Small Subset of GTEx Dataset | GTExsmall |
| Fitting reduced-rank ridge regression with given rank and shrinkage penalty | rrs.fit |