Package: idiffomix 1.0.0
idiffomix: Integrated Differential Analysis of Multi-Omics Data using a Joint Mixture Model
A joint mixture model is proposed that integrates information from gene expression data and methylation data at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of DMCs and DEGs. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm.
Authors:
idiffomix_1.0.0.tar.gz
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idiffomix.pdf |idiffomix.html✨
idiffomix/json (API)
NEWS
| # Install 'idiffomix' in R: |
| install.packages('idiffomix', repos = c('https://koyelucd.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/koyelucd/idiffomix/issues
- gene_chromosome_data - Data containing chromosome information and the genes located on them.
- gene_expression_data - Gene expression data for patients suffering from breast cancer
- methylation_data - Methylation array data for patients suffering from breast cancer
Last updated 4 months agofrom:2beadb29e1. Checks:1 OK, 8 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 15 2025 |
| R-4.5-win | WARNING | Mar 15 2025 |
| R-4.5-mac | WARNING | Mar 15 2025 |
| R-4.5-linux | WARNING | Mar 15 2025 |
| R-4.4-win | WARNING | Mar 15 2025 |
| R-4.4-mac | WARNING | Mar 15 2025 |
| R-4.4-linux | WARNING | Mar 15 2025 |
| R-4.3-win | WARNING | Mar 15 2025 |
| R-4.3-mac | WARNING | Mar 15 2025 |
Exports:data_transformationidiffomix
Dependencies:clicodetoolscolorspacecowplotcpp11doParalleldplyredgeRfansifarverforeachgenericsggplot2gluegridExtragtableisobanditeratorslabelinglatticelifecyclelimmalocfitmagrittrMASSMatrixmclustmgcvmunsellnlmepillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangscalesstatmodstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The function to filter, normalize and transform RNA-Seq and methylation data. | data_transformation |
| Data containing chromosome information and the genes located on them. | gene_chromosome_data |
| Gene expression data for patients suffering from breast cancer | gene_expression_data |
| The idiffomix function | idiffomix |
| Methylation array data for patients suffering from breast cancer | methylation_data |
| Plots for visualizing the idiffomix class object | plot.idiffomix |
