Table 1 Methods for the analysis of multi-omics datasets
From: Methods for the integration of multi-omics data: mathematical aspects
Method | Specificity | Multi-omics approach | Implementation |
|---|---|---|---|
Camelot [15] | Specific | Bivariate predictive regression model | NA |
CNAmet [19] | Specific | Multi-omics gene-wise scores | R |
FALDA [21] | General | FA + LDA of a joint matrix | NA |
Integromics [3] | General | Regularized CCA, sparse PLS | R |
iPAC [14] | Specific | Sequential | NA |
MCD [13] | Specific | Sequential | NA |
MCIA [20] | General | Multiple co-inertia analysis | R |
sMBPLS [4] | General | Sparse Multi-Block PLS regression | Matlab |
Coalesce [30] | Specific | Multi-omics probabilities | C ++ |
iCluster [12] | General | Joint Gaussian latent variable models | R |
MDI [28] | General | DMA mixture models | Matlab |
PSDF [29] | General | Hierarchical DMA mixture models | Matlab |
TMD [27] | General | Hierarchical DMA mixture models | Matlab |
Kernel Fusion [18] | General | Integration of omics-specific kernels | Matlab |
Endeavour [37] | General | Integration of omics-specific ranks with order statistics | Webserver |
MOO [16] | General | Sub-network extraction on MWG | R |
Multiplex [38] | General | Joint analysis of multi-layered networks | NA |
NuChart [35] | Specific | Analysis of a MWG | R |
SNF [17] | General | Similarity network fusion | Matlab, R |
SteinerNet [33] | Specific | Sub-network extraction on MWG | Webserver |
stSVM [34] | Specific | MWG | R |
Paradigm [51] | General | Multi-omics bayesian factor graphs | C ++ |
Conexic [11] | Specific | Sequential | Java |