/awesome-multi-omics

List of software packages for multi-omics analysis

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awesome-multi-omics

A community-maintained list of software packages for multi-omics data analysis.

While many of the packages here are marketed for "omics" data (transcriptomics, proteomics, etc.), other more general terms for this type of data analysis are:

  • multi-modal
  • multi-table
  • multi-way

The common thread among the methods listed here is that the same samples are measured across different assays. The data can be described as multiple matrices/tables with the same number of samples and varying number of features.

The repo is in the style of Sean Davis' awesome-single-cell repo for single-cell analysis methods.

Contributions welcome...

For brevity, below lists only the first author of multi-omics methods.

Software packages and methods

Multi-omics correlation or factor analysis

  • 2007 - SCCA - Parkhomenko - sparse CCA - paper 1, paper 2
  • 2008 - PCCA - Waaijenborg - penalized CCA / CCA-EN - paper
  • 2009 - PMA - Witten - Sparse Multi CCA - paper 1, paper 2
  • 2009 - sPLS - Lê Cao - sparse PLS - paper
  • 2009 - gesca - Hwang - RGSCA regularized generalized structured component analysis - paper
  • 2010 - Regularized dual CCA - Soneson - paper
  • 2011 - RGCCA - Tenenhaus - Regularized Generalized CCA and Sparse Generalized CCA - paper 1, paper 2
  • 2011 - SNMNMF - Zhang - Sparse Network-regularized Multiple Non-negative Matrix Factorization - paper
  • 2011 - scca - Lee - Sparse Canonical Covariance Analysis for High-throughput Data - paper
  • 2012 - STATIS/DiSTATIS - Abdi - structuring three-way statistical tables - paper
  • 2012 - joint NMF - Zhang - extension of NMF to multiple datasets - paper
  • 2012 - sMBPLS - Li - sparse MultiBlock Partial Least Squares - paper
  • 2012 - Bayesian group factor analysis - Virtanen - paper
  • 2012 - RIMBANET - Zhu - Reconstructing Integrative Molecular Bayesian Networks - paper
  • 2013 - FactoMineR - Abdi - MFA: multiple factor analysis - paper
  • 2013 - JIVE - Lock - joint & individual variance explained - paper
  • 2013 - pandaR - Schlauch - Passing Attributes between Networks for Data Assimilation - paper
  • 2014 - omicade4 - Meng - MCIA: multiple co-interia analysis - paper
  • 2014 - STATegRa - Planell - DISCO, JIVE, & O2PLS - paper
  • 2014 - Joint factor model - Ray - paper
  • 2014 - GFAsparse - Khan - group factor analysis sparse paper 1, paper 2
  • 2015 - Sparse CCA - Gao (3rd paper first author is Chen) - paper 1, paper 2, paper 3
  • 2015 - CCAGFA - Klami - Bayesian Canonical Correlation Analysis and Group Factor Analysis - paper 1, paper 2
  • 2016 - CMF - Klami - collective matrix factorization - paper
  • 2016 - moGSA - Meng - multi-omics gene set analysis - paper
  • 2016 - iNMF - Yang - integrative NMF - paper
  • 2016 - BASS - Zhao - Bayesian group factor analysis - paper
  • 2016 - imputeMFA in missMDA - Voillet - multiple imputation for multiple factor analysis (MI-MFA) - paper
  • 2016 - PLSCA - Beaton - Partial Least Square Correspondence Analysis - paper
  • 2017 - mixOmics - Rohart - various methods - paper1, paper2
  • 2017 - mixedCCA - Yoon - sparse CCA for data of mixed types - paper
  • 2017 - SLIDE - Gaynanova - Structural Learning and Integrative Decomposition of Multi-View Data - paper
  • 2017 - fCCAC - Madrigal - functional canonical correlation analysis to evaluate covariance - paper
  • 2017 - TSKCCA - Yoshida - Sparse kernel canonical correlation analysis - paper
  • 2017 - SMSMA - Kawaguchi - Supervised multiblock sparse multivariable analysis - paper
  • 2018 - AJIVE - Feng - angle-based JIVE - paper
  • 2018 - MOFA - Argelaguet - multi-omics factor analysis - paper 1, paper 2, application
  • 2018 - PCA+CCA - Brown - paper
  • 2018 - JACA - Zhang - Joint Association and Classification Analysis - paper
  • 2018 - iPCA - Tang - Integrated Principal Components Analysis - paper
  • 2018 - pCIA - Min - penalized COI - paper
  • 2018 - sSCCA - Safo - structured sparse CCA - paper
  • 2018 - SWCCA - Min - Sparse Weighted CCA - paper
  • 2018 - OmicsPLS - Bouhaddani - O2PLS implemented in R, with an alternative cross-validation scheme - paper
  • 2018 - SCCA-BC - Pimentel - Biclustering by sparse canonical correlation analysis - paper
  • 2019 - WON-PARAFAC - Kim - weighted orthogonal nonnegative parallel factor analysis - paper
  • 2019 - BIDIFAC - Park - bidimensional integrative factorization - paper 1, paper 2
  • 2019 - SmCCNet - Shi - sparse multiple canonical correlation network analysis - paper
  • 2020 - msPLS - Csala - multiset sparse partial least squares path modeling - paper
  • 2020 - MOTA - Fan - network-based multi-omic data integration for biomarker discovery - paper
  • 2020 - D-CCA - Shu - Decomposition-based Canonical Correlation Analysis - paper
  • 2020 - COMBI - Hawinkel - Compositional Omics Model-Based Integration - paper
  • 2020 - DPCCA - Gundersen - Deep Probabilistic CCA - paper
  • 2020 - MEFISTO - Velten - spatial or temporal relationships - preprint
  • 2020 - MultiPower - Tarazona - Sample size in multi-omic experiments - paper
  • 2020 - mixedCCA - Yoon - Sparse semiparametric CCA for data of mixed types - paper

Ecology multi-table literature

  • 1994 - COI - Doledec - Co‐inertia analysis - paper
  • 2007 - ade4 - Dray - Implementing the Duality Diagram for Ecologists - paper

Chemometrics multi-table literature

  • 1987 - - Wold - Multi‐way principal components‐and PLS‐analysis - paper
  • 1996 - - Wold - Hierarchical multiblock PLS - paper
  • 2003 - - Trygg - O2‐PLS, a two‐block (X–Y) latent variable regression (LVR) - paper
  • 2011 - - Hanafi - Connections between multiple COI and consensus PCA - paper
  • 2015 - THEME - Verron - THEmatic Model Exploration - paper

Behavioral research multi-table literature

  • 2013 - DISCO SCA - Schouteden - distinctive and common components with simultaneous-component analysis - paper 1, paper 2

Multi-omics clustering / classification / prediction

Note: I think that prediction of genomic tracks, e.g. ChIP-seq, from other genomic tracks is a large area of research that may deserve a separate repository. Below are methods for clustering / classification of samples into sub-types or prediction of outcomes.

Multi-omics autoencoders

  • 2019 - maui - Ronen - Stacked VAE + clustering predictive of survival - paper
  • 2019 - IntegrativeVAEs - Simidjievski - Variational autoencoders + classification - paper
  • 2021 - DeepProg - Poirion - DL and ML ensemble + survival prediction - paper
  • 2021 - SHAE - Wissel - Supervised Hierarchical Autoencoder + survival prediction - preprint

Multi-omics networks

  • 2018 - MolTi-DREAM - Didier - identifying communities from multiplex networks, and annotated the obtained clusters article
  • 2019 - RWR-MH - Valdeolivas - Random walk with restart on multiplex and heterogeneous biological networks article
  • 2020 - MOGAMUN - Novoa-del-toro - A multi-objective genetic algorithm to find active modules in multiplex biological networks preprint
  • 2021 - RWRF - Wen - Random Walk with Restart for multi-dimensional data Fusion paper

Single cell multi-omics

  • 2018 - cardelino - - gene expression states to clones (SNVs from scRNA-seq + bulk exome data) -
  • 2018 - clonealign - Campbell - gene expression states to clones (scRNA-seq + scDNA-seq (CNV)) - paper
  • 2020 - CiteFuse - Kim - CITE-seq data analysis paper
  • 2021 - CoSpar - Wang - infer dynamics by integrating state and lineage information - paper

Multi-study correlation or factor analysis

  • 2016 - MSFA - De Vito - multi-study factor analysis: same features, different samples - paper

Multi-omics reviews / evaluations

Multi-omics application papers

Multi-omics data management

Meetings and workshops