Package: easyEWAS 1.0.1
easyEWAS: Perform and Visualize EWAS Analysis
Tools for conducting epigenome-wide association studies (EWAS) and visualizing results. Users provide sample metadata and methylation matrices to run EWAS with linear models, linear mixed-effects models, or Cox models. The package supports downstream visualization, bootstrap validation, enrichment analysis, batch effect correction, and differentially methylated region (DMR) analysis with optional parallel computing. Methods are described in Wang et al. (2025) <doi:10.1093/bioadv/vbaf026>, Johnson et al. (2007) <doi:10.1093/biostatistics/kxj037>, and Peters et al. (2015) <doi:10.1186/1756-8935-8-6>.
Authors:
easyEWAS_1.0.1.tar.gz
easyEWAS_1.0.1.zip(r-4.7-any)easyEWAS_1.0.1.zip(r-4.6-any)easyEWAS_1.0.1.zip(r-4.5-any)
easyEWAS_1.0.1.tgz(r-4.6-any)easyEWAS_1.0.1.tgz(r-4.5-any)
easyEWAS_1.0.1.tar.gz(r-4.7-any)easyEWAS_1.0.1.tar.gz(r-4.6-any)
easyEWAS_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
easyEWAS/json (API)
| # Install 'easyEWAS' in R: |
| install.packages('easyEWAS', repos = c('https://ytwangzero.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ytwangzero/easyewas/issues
Pkgdown/docs site:https://easyewas-tutorial.github.io
- methydata - Example Methylation Matrix
- sampledata - Example Sample Metadata
Last updated from:93910999b4. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 1168 | ||
| source / vignettes | OK | 1766 | ||
| linux-release | OK | 1305 | ||
| macos-release | OK | 1401 | ||
| macos-oldrel | OK | 1191 | ||
| windows-devel | OK | 730 | ||
| windows-release | OK | 1067 | ||
| windows-oldrel | OK | 925 | ||
| wasm-release | OK | 1377 |
Exports:batchEWASbootEWASdmrEWASdownloadAnnotEWASenrichEWASinitEWASloadEWASplotEWASstartEWAStransEWAS
Dependencies:askpassbackportsbase64encbitbit64bootbslibcachemcellrangercheckmateclicliprCMplotcodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableddpcrdigestdoParalleldplyrDTevaluatefarverfastmapfontawesomeforeachfsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4lmerTestlubridatemagrittrMASSMatrixmemoisemimeminqamixtoolsnlmenloptrnumDerivopensslotelpillarpkgconfigplotlyplyrprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreadxlreformulasrematchrlangrmarkdownS7sassscalessegmentedshinyshinydisconnectshinyjssourcetoolsstringistringrsurvivalsystibbletictoctidyrtidyselecttimechangetinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Perform batch effect correction | batchEWAS |
| Perform Bootstrap-based Internal Validation | bootEWAS |
| Perform Differentially Methylated Region analysis | dmrEWAS |
| Download and cache chip annotation tables | downloadAnnotEWAS |
| Enrichment analyses | enrichEWAS |
| EWAS Model Computation Utilities | ewasfun_cox ewasfun_lm ewasfun_lmer |
| Initialize the EWAS module | initEWAS |
| Load all data files for EWAS module | loadEWAS |
| Example Methylation Matrix | methydata |
| Visualize the results of EWAS analysis | plotEWAS |
| Example Sample Metadata | sampledata |
| Perform EWAS Analysis | startEWAS |
| Convert variable type of sample data | transEWAS |