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-4.5)omicwas_0.8.0.zip(r-4.4)omicwas_0.8.0.zip(r-4.3)
omicwas_0.8.0.tgz(r-4.4-any)omicwas_0.8.0.tgz(r-4.3-any)
omicwas_0.8.0.tar.gz(r-4.5-noble)omicwas_0.8.0.tar.gz(r-4.4-noble)
omicwas_0.8.0.tgz(r-4.4-emscripten)omicwas_0.8.0.tgz(r-4.3-emscripten)
omicwas.pdf |omicwas.html✨
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
- GSE42861small - Small Subset of GSE42861 Dataset From GEO
- GSE79262small - Small Subset of GSE79262 Dataset From GEO
- GTExsmall - Small Subset of GTEx Dataset
Last updated 4 years agofrom:1852179a55. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | OK | Nov 18 2024 |
| R-4.5-linux | OK | Nov 18 2024 |
| R-4.4-win | OK | Nov 18 2024 |
| R-4.4-mac | OK | Nov 18 2024 |
| R-4.3-win | OK | Nov 18 2024 |
| R-4.3-mac | OK | Nov 18 2024 |
Exports:ctassocctcisQTLrrs.fit
Dependencies:backportsbitbroomclicodetoolscpp11data.tabledplyrfansiffforeachgenericsglmnetglueiteratorslatticelifecyclemagrittrMASSMatrixmatrixStatspillarpkgconfigpurrrR6RcppRcppEigenrlangshapestringistringrsurvivaltibbletidyrtidyselectutf8vctrswithr
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 |
