4. Data input for MethylMix | 5. Running MethylMix | 6. Graphical output | 7. References | 8. Sesssion Info
Package: MethylMix 2.43.0
Olivier Gevaert
MethylMix: MethylMix: Identifying methylation driven cancer genes
MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.
Authors:
MethylMix_2.43.0.tar.gz
MethylMix_2.43.0.zip(r-4.7)MethylMix_2.43.0.zip(r-4.6)MethylMix_2.43.0.zip(r-4.5)
MethylMix_2.43.0.tgz(r-4.6-any)MethylMix_2.43.0.tgz(r-4.5-any)
MethylMix_2.43.0.tar.gz(r-4.7-any)MethylMix_2.43.0.tar.gz(r-4.6-any)
MethylMix_2.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MethylMix/json (API)
| # Install 'MethylMix' in R: |
| install.packages('MethylMix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- BatchData - BatchData data set
- GEcancer - Cancer Gene expression data of glioblastoma patients from the TCGA project
- METcancer - DNA methylation data from cancer tissue from glioblastoma patients from the TCGA project
- METnormal - DNA methylation data from normal tissue from glioblastoma patients
- ProbeAnnotation - ProbeAnnotation data set
- SNPprobes - SNPprobes data set
On BioConductor:MethylMix-2.43.0(bioc 3.24)MethylMix-2.42.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dnamethylationstatisticalmethoddifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetwork
Last updated from:2a9a439bfb. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 158 | ||
| linux-devel-x86_64 | NOTE | 212 | ||
| source / vignettes | OK | 183 | ||
| linux-release-x86_64 | NOTE | 250 | ||
| macos-release-arm64 | NOTE | 158 | ||
| macos-oldrel-arm64 | NOTE | 116 | ||
| windows-devel | NOTE | 165 | ||
| windows-release | NOTE | 156 | ||
| windows-oldrel | NOTE | 166 | ||
| wasm-release | OK | 112 |
Exports:ClusterProbesDownload_DNAmethylationDownload_GeneExpressionGetDataMethylMixMethylMix_ModelGeneExpressionMethylMix_PlotModelMethylMix_PredictPreprocess_DNAmethylationPreprocess_GeneExpression
Dependencies:bitopscliclustercodetoolscpp11data.tabledigestfarverforeachggplot2gluegtableimputeisobanditeratorslabelinglifecyclelimmaR.matlabR.methodsS3R.ooR.utilsR6RColorBrewerRCurlrlangRPMMS7scalesstatmodvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BatchData data set | BatchData |
| The ClusterProbes function | ClusterProbes |
| The Download_DNAmethylation function | Download_DNAmethylation |
| The Download_GeneExpression function | Download_GeneExpression |
| Cancer Gene expression data of glioblastoma patients from the TCGA project | GEcancer |
| The GetData function | GetData |
| DNA methylation data from cancer tissue from glioblastoma patients from the TCGA project | METcancer |
| MethylMix: Mixture model for DNA methylation data in cancer. | MethylMix |
| The MethylMix_ModelGeneExpression function | MethylMix_ModelGeneExpression |
| The MethylMix_PlotModel function. | MethylMix_PlotModel |
| The MethylMix_Predict function | MethylMix_Predict |
| DNA methylation data from normal tissue from glioblastoma patients | METnormal |
| The predictOneGene function | predictOneGene |
| The Preprocess_DNAmethylation function | Preprocess_DNAmethylation |
| The Preprocess_GeneExpression function | Preprocess_GeneExpression |
| ProbeAnnotation data set | ProbeAnnotation |
| SNPprobes data set | SNPprobes |
