MIMOmics has developed several methods for the analysis of (multiple) omics datasets. For many methods code has been made available our MIMOmics github (https://github.com/mimomics). For some methods user-friendly R packages, Java interfaces, Python libraries or programs in C++ have been developed. For other methods just code has been made available:
- Glycanr A R package for analysing N-Glycan Data. Useful utilities in N-glycan data analysis. This package tries to fill the gap in N-glycan data analysis by providing easy to use functions for basic operations on data (see https://en.wikipedia.org/wiki/Glycomicsfor more details on Glycomics).
- R-code for construction of networks regarding specific covariates.
Sparse Supervised Gaussian methods
- SSG Python Library to run various methods, to visualise the learned models, and to compute performance indices.
Data integration and dimension reduction
- OmicsPLS R-package which performs O2PLS data integration method for two datasets yielding joint and data-specific parts for each dataset. The algorithm automatically switches to a memory-efficient approach to fit O2PLS to high dimensional data.
- R code to perform Probabilistic Partial Least Squares.
Prediction using omics datasets
- Augmented prediction. R code to perform constrained regularized regression to determine added value of one omic dataset on top of another omic dataset.
- PredNet. R code for combining network and prediction models to obtain stable and better interpretable prediction models.
Genome Wide Association Analysis
- MultiABEL R package to perform Multi-Trait GWAS.
- ProABEL C++ code for genome-wide association analysis of imputed genetic data.
- OmicABELnoMM C++ code for a high-performance computing algorithm for linear regression of omics data.
- OmicABEL C code for high-performance implementation of genome-wide association analysis using mixed models.
Using the geneXplain platform, an online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications
- geneXplainr a R-package which provides an R client for the geneXplain platform.
- geneXplain API a Java programming interface.