awesome-multi-omics

Multi-omics analysis library

A collection of software packages for analyzing multi-omics data from different assays.

List of software packages for multi-omics analysis

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awesome-multi-omics / Software packages and methods / Multi-omics correlation or factor analysis
paper 1 2007 - - Parkhomenko - sparse CCA - ,
paper 2008 - - Waaijenborg - penalized CCA / CCA-EN -
PMA 2009 - - Witten - Sparse Multi CCA - ,
paper 2009 - - Lê Cao - sparse PLS -
gesca 2009 - - Hwang - RGSCA regularized generalized structured component analysis -
paper 2010 - - Soneson -
RGCCA 2011 - - Tenenhaus - Regularized Generalized CCA and Sparse Generalized CCA - ,
paper 2011 - - Zhang - Sparse Network-regularized Multiple Non-negative Matrix Factorization -
scca 1 over 7 years ago 2011 - - Lee - Sparse Canonical Covariance Analysis for High-throughput Data -
STATIS/DiSTATIS 4 about 1 year ago 2012 - - Abdi - structuring three-way statistical tables -
paper 2012 - - Zhang - extension of NMF to multiple datasets -
paper 2012 - - Li - sparse MultiBlock Partial Least Squares -
paper 2012 - - Virtanen -
RIMBANET 2012 - - Zhu - Reconstructing Integrative Molecular Bayesian Networks -
FactoMineR 2013 - - Abdi - MFA: multiple factor analysis -
JIVE 2013 - - Lock - joint & individual variance explained -
pandaR 2013 - - Schlauch - Passing Attributes between Networks for Data Assimilation -
omicade4 2014 - - Meng - MCIA: multiple co-interia analysis -
STATegRa 2014 - - Planell - DISCO, JIVE, & O2PLS -
paper 2014 - - Ray -
GFAsparse 2014 - - Khan - group factor analysis sparse ,
paper 1 2015 - - Gao (3rd paper first author is Chen) - , ,
CCAGFA 2015 - - Klami - Bayesian Canonical Correlation Analysis and Group Factor Analysis - ,
CMF 2016 - - Klami - collective matrix factorization -
moGSA 2016 - - Meng - multi-omics gene set analysis -
iNMF 16 over 6 years ago 2016 - - Yang - integrative NMF -
BASS 20 almost 9 years ago 2016 - - Zhao - Bayesian group factor analysis -
missMDA 2016 - in - Voillet - multiple imputation for multiple factor analysis (MI-MFA) -
PLSCA 1 almost 8 years ago 2016 - - Beaton - Partial Least Square Correspondence Analysis -
mixOmics 2017 - - Rohart - various methods - ,
mixedCCA 20 about 2 years ago 2017 - - Yoon - sparse CCA for data of mixed types -
SLIDE 7 over 3 years ago 2017 - - Gaynanova - Structural Learning and Integrative Decomposition of Multi-View Data -
fCCAC 0 over 2 years ago 2017 - - Madrigal - functional canonical correlation analysis to evaluate covariance -
TSKCCA 6 over 6 years ago 2017 - - Yoshida - Sparse kernel canonical correlation analysis -
paper 2017 - - Kawaguchi - Supervised multiblock sparse multivariable analysis -
AJIVE 4 8 months ago 2018 - - Feng - angle-based JIVE -
MOFA 235 about 4 years ago 2018 - - Argelaguet - multi-omics factor analysis - , ,
PCA+CCA 18 almost 6 years ago 2018 - - Brown -
JACA 3 over 3 years ago 2018 - - Zhang - Joint Association and Classification Analysis -
paper 2018 - - Tang - Integrated Principal Components Analysis -
pCIA 2018 - - Min - penalized COI -
paper 2018 - - Safo - structured sparse CCA -
paper 2018 - - Min - Sparse Weighted CCA -
OmicsPLS 31 over 2 years ago 2018 - - Bouhaddani - O2PLS implemented in R, with an alternative cross-validation scheme -
SCCA-BC 2 over 9 years ago 2018 - - Pimentel - Biclustering by sparse canonical correlation analysis -
mixKernel 2018 - - Mariette - kernel method for unsupervised multi-omics integration - ,
WON-PARAFAC 1 over 3 years ago 2019 - - Kim - weighted orthogonal nonnegative parallel factor analysis -
BIDIFAC 3 7 months ago 2019 - - Park - bidimensional integrative factorization - ,
SmCCNet 2019 - - Shi - sparse multiple canonical correlation network analysis -
msPLS 1 over 3 years ago 2020 - - Csala - multiset sparse partial least squares path modeling -
paper 2020 - - Fan - network-based multi-omic data integration for biomarker discovery -
D-CCA 11 over 2 years ago 2020 - - Shu - Decomposition-based Canonical Correlation Analysis -
COMBI 2020 - - Hawinkel - Compositional Omics Model-Based Integration -
DPCCA 25 over 3 years ago 2020 - - Gundersen - Deep Probabilistic CCA -
MEFISTO 2020 - - Velten - spatial or temporal relationships -
MultiPower 30 over 1 year ago 2020 - - Tarazona - Sample size in multi-omic experiments -
mixedCCA 2020 - - Yoon - Sparse semiparametric CCA for data of mixed types -
smCIA/ssmCIA 2020 - - Min - Sparse (structured sparse) multiple co-Inertia analysis -
MuVI 29 5 months ago 2023 - - Qoku - Integrate noisy feature sets -

awesome-multi-omics / Software packages and methods / Ecology multi-table literature
paper 1994 - - Doledec - Co‐inertia analysis -
ade4 2007 - - Dray - Implementing the Duality Diagram for Ecologists -

awesome-multi-omics / Software packages and methods / Chemometrics multi-table literature
paper 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 -
THEME 1 about 1 year ago 2015 - - Verron - THEmatic Model Exploration -

awesome-multi-omics / Software packages and methods / Behavioral research multi-table literature
paper 1 2013 - DISCO SCA - Schouteden - distinctive and common components with simultaneous-component analysis - ,

awesome-multi-omics / Software packages and methods / Multi-omics clustering / classification / prediction
iCluster 2009 - - Shen -
PSDF 2011 - - Yuan - Data fusion by Bayesian nonparametric Dirichlet modeling - ,
MDI 2012 - - Kirk - ,
iClusterPlus 2013 - - Mo -
BCC 19 over 1 year ago 2013 - - Lock - Bayesian consensus clustering -
iBAG 5 about 5 years ago 2013 - - Wang - Integrative Bayesian Analysis of Genomics -
SNF 2014 - - Wang -
paper 2015 - moCluster - Meng - Derivative of iClusterPlus -
clusternomics 2017 - - Gabasova -
publication 2017 - PFA - Shi - Pattern Fussion analysis -
IBOOST 2019 - - Wong -
Spectrum 2019 - - John -
NEMO 15 over 4 years ago 2019 - - Rappoport - Similarity-based Clustering -
INF 2020 - - Chierici and Bussola -
ClustOmics 5 almost 3 years ago 2021 - - Brière - Consensus clustering -
MOGONET 143 over 3 years ago 2021 - - Tongxin Wang - Multi-Omics Graph cOnvolutional NETworks -

awesome-multi-omics / Software packages and methods / Multi-omics autoencoders
maui 48 over 1 year ago 2019 - - Ronen - Stacked VAE + clustering predictive of survival -
IntegrativeVAEs 27 about 3 years ago 2019 - - Simidjievski - Variational autoencoders + classification -
OmiVAE 31 over 3 years ago 2019 - - Xiaoyu Zhang - Integrated Multi-omics Analysis Using Variational Autoencoders -
DeepProg 76 11 months ago 2021 - - Poirion - DL and ML ensemble + survival prediction -
SHAE 2021 - - Wissel - Supervised Hierarchical Autoencoder + survival prediction -

awesome-multi-omics / Software packages and methods / Multi-omics networks
MolTi-DREAM 3 about 6 years ago 2018 - - Didier - identifying communities from multiplex networks, and annotated the obtained clusters
NetICS 15 over 3 years ago 2018 - Christos Dimitrakopoulos - Network-based integration of multi-omics data for prioritizing cancer genes -
RWR-MH 34 over 4 years ago 2019 - - Valdeolivas - Random walk with restart on multiplex and heterogeneous biological networks
MOGAMUN 2020 - - Novoa-del-toro - A multi-objective genetic algorithm to find active modules in multiplex biological networks
RWRF 7 about 4 years ago 2021 - - Wen - Random Walk with Restart for multi-dimensional data Fusion

awesome-multi-omics / Software packages and methods / Single cell multi-omics
cardelino 59 about 2 years ago 2018 - - - gene expression states to clones (SNVs from scRNA-seq + bulk exome data) -
clonealign 32 almost 4 years ago 2018 - - Campbell - gene expression states to clones (scRNA-seq + scDNA-seq (CNV)) -
CiteFuse 2020 - - Kim - CITE-seq data analysis
CoSpar 2021 - - Wang - infer dynamics by integrating state and lineage information -

awesome-multi-omics / Software packages and methods / Multi-study correlation or factor analysis
MSFA 2 over 2 years ago 2016 - - De Vito - multi-study factor analysis: same features, different samples -

awesome-multi-omics / Software packages and methods / Multi-omics simulation
InterSIM 2016 - - Chalise - methylation, gene expression and protein expression -
MOSim 2019 - - Martinez-Mira - RNA-seq, ATAC-seq (DNase-seq), ChIP-seq, small RNA-seq and Methyl-seq. -
OmicsSIMLA 2019 - - Chung - DNA, CNV, WGBS, RNAseq, Protein expression -

awesome-multi-omics / Multi-omics reviews / evaluations
Multivariate data analysis: The French way 2008 - Holmes -
A practical data processing workflow for multi-OMICS projects 2014 - Kohl -
Measuring multivariate association and beyond 2016 - Josse -
Multi-omic data integration enables discovery of hidden biological regularities 2016 - Ebrahim -
Dimension reduction techniques for the integrative analysis of multi-omics data 2016 - Meng -
A review on machine learning principles for multi-view biological data integration 2016 - Li -
More Is Better: Recent Progress in Multi-Omics Data Integration Methods 2017 - Huang -
Multi-omics approaches to disease 2017 - Hasin -
Statistical data integration: Challenges and opportunities 2017 - Allen -
Multi-omic and multi-view clustering algorithms: review and cancer benchmark 2018 - Rappoport -
Current multiblock methods: Competition or complementarity? A comparative study in a unified framework 2018 - Bougeard -
Integrative omics for health and disease 2018 - Karczewski -
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data 2018 - Yan -
Integrated omics: tools, advances and future approaches 2019 - Misra -
Evaluation of integrative clustering methods for the analysis of multi-omics data 2019 - Chauvel -
Consistency and overfitting of multi-omics methods on experimental data 2019 - McCabe - -
Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration 2019 - Pierre-Jean -
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community 2019 - Pinu -
A Selective Review of Multi-Level Omics Data Integration Using Variable Selection 2019 - Wu -
Multitable methods for microbiome data integration 2019 - Sankaran - -
Heterogeneous Multi-Layered Network Model for Omics Data Integration and Analysis 2020 - Lee -
Large-scale benchmark study of survival prediction methods using multi-omics data 2020 - Herrmann - -
Multiview learning for understanding functional multiomics 2020 - Nguyen -
Metabolomics and multi-omics integration: a survey of computational methods and resources 2020 - Eicher -
Benchmarking joint multi-omics dimensionality reduction approaches for cancer study 2020 - Cantini -
Multi-omics Data Integration, Interpretation, and Its Application 2020 - Subramanian -
State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing 2020 - Krassowski - -
Data-Driven Modeling of Pregnancy-Related Complications 2021 - Espinosa -
Uncovering Cross-Cohort Molecular Features with Multi-Omics Integration Analysis 2022 - Jiang -
Machine learning for multi-omics data integration in cancer 2022 - Cai -

awesome-multi-omics / Multi-omics application papers
A multivariate analysis approach to the integration of proteomic and gene expression data 2007 - Fagan -
The duality diagram in data analysis: Examples of modern applications 2011 - De la Cruz - -
Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data 2014 - Tomescu -
A community effort to assess and improve drug sensitivity prediction algorithms 2014 - Costello (NCI/DREAM) -
Inferring gene–gene interactions and functional modules using sparse canonical correlation analysis 2015 - Wang -
TCGA2STAT: simple TCGA data access for integrated statistical analysis in R 2016 - Wan - -
Integrating single-cell transcriptomic data across different conditions, technologies, and species. 2017 - Butler -
Reference trait analysis reveals correlations between gene expression and quantitative traits in disjoint samples 2018 - Skelly - -
Comprehensive integration of single cell data 2018 - Stuart -
Joint analysis of gene expression levels and histological images identifies genes associated with tissue morphology 2018 - Ash -
Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data 2019 - Xu -
Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy 2019 - Ghaemi - Multi-omics in pregnancy using stacked generalization

awesome-multi-omics / Multi-omics data management
MultiAssayExperiment 2017 - - Ramos - Software for the integration of multi-omics experiments in Bioconductor -
muon 218 22 days ago 2021 - - Bredikhin -

awesome-multi-omics / Batch effect correction
MultiBaC 5 almost 3 years ago 2020 - - Ugidos - and
A multivariate method to correct for batch effects in microbiome data

awesome-multi-omics / Meetings and workshops
Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Types 2020 - - - June 14-19, 2020 in Banff, Canada

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