List of software packages for multi-omics data analysis. A shameless clone of Sean Davis' awesome-single-cell repo.
- 2009 - Sparse mCCA - paper 1, paper 2
- 2010 - Regularized dual CCA - paper
- 2013 - JIVE - joint & individual variance explained - paper
- 2014 - MCIA - multiple co-interia analysis - paper
- 2014 - RGCCA - Regularized generalized CCA - paper
- 2016 - Bayesian group factor analysis - paper
- 2016 - MSFA - multi-study factor analysis, unlike the other methods here, this is for same feature, different samples - paper
- 2016 - moGSA - paper
- 2017 - mixOmics - paper
- 2018 - AJIVE - angle-based JIVE - paper
- 2018 - MOFA - multi-omics factor analysis - paper
- 2018 - PCA+CCA - paper
- ...
- 2018 - cardelino - assign gene expression states to clones by integrating SNVs from scRNA-seq with bulk exome data
- 2018 - clonealign - assign gene expression states to clones by integrating scRNA-seq with scDNA-seq (CNV) data - paper
- 2014 - A practical data processing workflow for multi-OMICS projects
- 2016 - Multi-omic data integration enables discovery of hidden biological regularities
- 2016 - Dimension reduction techniques for the integrative analysis of multi-omics data - from omicade4 and moGSA authors
- 2017 - More Is Better: Recent Progress in Multi-Omics Data Integration Methods
- 2017 - Multi-omics approaches to disease
- 2018 - MOVIE: Multi-Omics VIsualization of Estimated contributions - code