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 12007 - - Parkhomenko - sparse CCA - ,
paper2008 - - Waaijenborg - penalized CCA / CCA-EN -
PMA2009 - - Witten - Sparse Multi CCA - ,
paper2009 - - Lê Cao - sparse PLS -
gesca2009 - - Hwang - RGSCA regularized generalized structured component analysis -
paper2010 - - Soneson -
RGCCA2011 - - Tenenhaus - Regularized Generalized CCA and Sparse Generalized CCA - ,
paper2011 - - Zhang - Sparse Network-regularized Multiple Non-negative Matrix Factorization -
scca1over 9 years ago2011 - - Lee - Sparse Canonical Covariance Analysis for High-throughput Data -
STATIS/DiSTATIS4almost 3 years ago2012 - - Abdi - structuring three-way statistical tables -
paper2012 - - Zhang - extension of NMF to multiple datasets -
paper2012 - - Li - sparse MultiBlock Partial Least Squares -
paper2012 - - Virtanen -
RIMBANET2012 - - Zhu - Reconstructing Integrative Molecular Bayesian Networks -
FactoMineR2013 - - Abdi - MFA: multiple factor analysis -
JIVE2013 - - Lock - joint & individual variance explained -
pandaR2013 - - Schlauch - Passing Attributes between Networks for Data Assimilation -
omicade42014 - - Meng - MCIA: multiple co-interia analysis -
STATegRa2014 - - Planell - DISCO, JIVE, & O2PLS -
paper2014 - - Ray -
GFAsparse2014 - - Khan - group factor analysis sparse ,
paper 12015 - - Gao (3rd paper first author is Chen) - , ,
CCAGFA2015 - - Klami - Bayesian Canonical Correlation Analysis and Group Factor Analysis - ,
CMF2016 - - Klami - collective matrix factorization -
moGSA2016 - - Meng - multi-omics gene set analysis -
iNMF17about 8 years ago2016 - - Yang - integrative NMF -
BASS20over 10 years ago2016 - - Zhao - Bayesian group factor analysis -
missMDA2016 - in - Voillet - multiple imputation for multiple factor analysis (MI-MFA) -
PLSCA1over 9 years ago2016 - - Beaton - Partial Least Square Correspondence Analysis -
mixOmics2017 - - Rohart - various methods - ,
mixedCCA20about 4 years ago2017 - - Yoon - sparse CCA for data of mixed types -
SLIDE7about 5 years ago2017 - - Gaynanova - Structural Learning and Integrative Decomposition of Multi-View Data -
fCCAC0over 4 years ago2017 - - Madrigal - functional canonical correlation analysis to evaluate covariance -
TSKCCA6over 8 years ago2017 - - Yoshida - Sparse kernel canonical correlation analysis -
paper2017 - - Kawaguchi - Supervised multiblock sparse multivariable analysis -
AJIVE4over 2 years ago2018 - - Feng - angle-based JIVE -
MOFA233almost 6 years ago2018 - - Argelaguet - multi-omics factor analysis - , ,
PCA+CCA18almost 8 years ago2018 - - Brown -
JACA3over 5 years ago2018 - - Zhang - Joint Association and Classification Analysis -
paper2018 - - Tang - Integrated Principal Components Analysis -
pCIA2018 - - Min - penalized COI -
paper2018 - - Safo - structured sparse CCA -
paper2018 - - Min - Sparse Weighted CCA -
OmicsPLS32about 4 years ago2018 - - Bouhaddani - O2PLS implemented in R, with an alternative cross-validation scheme -
SCCA-BC2over 11 years ago2018 - - Pimentel - Biclustering by sparse canonical correlation analysis -
mixKernel2018 - - Mariette - kernel method for unsupervised multi-omics integration - ,
WON-PARAFAC1over 5 years ago2019 - - Kim - weighted orthogonal nonnegative parallel factor analysis -
BIDIFAC3over 2 years ago2019 - - Park - bidimensional integrative factorization - ,
SmCCNet2019 - - Shi - sparse multiple canonical correlation network analysis -
msPLS1over 5 years ago2020 - - Csala - multiset sparse partial least squares path modeling -
paper2020 - - Fan - network-based multi-omic data integration for biomarker discovery -
D-CCA11about 4 years ago2020 - - Shu - Decomposition-based Canonical Correlation Analysis -
COMBI2020 - - Hawinkel - Compositional Omics Model-Based Integration -
DPCCA25over 5 years ago2020 - - Gundersen - Deep Probabilistic CCA -
MEFISTO2020 - - Velten - spatial or temporal relationships -
MultiPower30over 3 years ago2020 - - Tarazona - Sample size in multi-omic experiments -
mixedCCA2020 - - Yoon - Sparse semiparametric CCA for data of mixed types -
smCIA/ssmCIA2020 - - Min - Sparse (structured sparse) multiple co-Inertia analysis -
MuVI27over 1 year ago2023 - - Qoku - Integrate noisy feature sets -

awesome-multi-omics / Software packages and methods / Ecology multi-table literature

paper1994 - - Doledec - Co‐inertia analysis -
ade42007 - - Dray - Implementing the Duality Diagram for Ecologists -

awesome-multi-omics / Software packages and methods / Chemometrics multi-table literature

paper1987 - - Wold - Multi‐way principal components‐and PLS‐analysis -
paper1996 - - Wold - Hierarchical multiblock PLS -
paper2003 - - Trygg - O2‐PLS, a two‐block (X–Y) latent variable regression (LVR) -
paper2011 - - Hanafi - Connections between multiple COI and consensus PCA -
THEME1almost 3 years ago2015 - - Verron - THEmatic Model Exploration -

awesome-multi-omics / Software packages and methods / Behavioral research multi-table literature

paper 12013 - DISCO SCA - Schouteden - distinctive and common components with simultaneous-component analysis - ,

awesome-multi-omics / Software packages and methods / Multi-omics clustering / classification / prediction

iCluster2009 - - Shen -
PSDF2011 - - Yuan - Data fusion by Bayesian nonparametric Dirichlet modeling - ,
MDI2012 - - Kirk - ,
iClusterPlus2013 - - Mo -
BCC19over 3 years ago2013 - - Lock - Bayesian consensus clustering -
iBAG5about 7 years ago2013 - - Wang - Integrative Bayesian Analysis of Genomics -
SNF2014 - - Wang -
paper2015 - moCluster - Meng - Derivative of iClusterPlus -
clusternomics2017 - - Gabasova -
publication2017 - PFA - Shi - Pattern Fussion analysis -
IBOOST2019 - - Wong -
Spectrum2019 - - John -
NEMO15over 6 years ago2019 - - Rappoport - Similarity-based Clustering -
INF2020 - - Chierici and Bussola -
ClustOmics5over 4 years ago2021 - - Brière - Consensus clustering -
MOGONET144over 5 years ago2021 - - Tongxin Wang - Multi-Omics Graph cOnvolutional NETworks -

awesome-multi-omics / Software packages and methods / Multi-omics autoencoders

maui49about 3 years ago2019 - - Ronen - Stacked VAE + clustering predictive of survival -
IntegrativeVAEs27almost 5 years ago2019 - - Simidjievski - Variational autoencoders + classification -
OmiVAE31about 5 years ago2019 - - Xiaoyu Zhang - Integrated Multi-omics Analysis Using Variational Autoencoders -
DeepProg77over 2 years ago2021 - - Poirion - DL and ML ensemble + survival prediction -
SHAE2021 - - Wissel - Supervised Hierarchical Autoencoder + survival prediction -

awesome-multi-omics / Software packages and methods / Multi-omics networks

MolTi-DREAM3almost 8 years ago2018 - - Didier - identifying communities from multiplex networks, and annotated the obtained clusters
NetICS15about 5 years ago2018 - Christos Dimitrakopoulos - Network-based integration of multi-omics data for prioritizing cancer genes -
RWR-MH36over 6 years ago2019 - - Valdeolivas - Random walk with restart on multiplex and heterogeneous biological networks
MOGAMUN2020 - - Novoa-del-toro - A multi-objective genetic algorithm to find active modules in multiplex biological networks
RWRF7about 6 years ago2021 - - Wen - Random Walk with Restart for multi-dimensional data Fusion

awesome-multi-omics / Software packages and methods / Single cell multi-omics

cardelino59almost 4 years ago2018 - - - gene expression states to clones (SNVs from scRNA-seq + bulk exome data) -
clonealign32almost 6 years ago2018 - - Campbell - gene expression states to clones (scRNA-seq + scDNA-seq (CNV)) -
CiteFuse2020 - - Kim - CITE-seq data analysis
CoSpar2021 - - Wang - infer dynamics by integrating state and lineage information -

awesome-multi-omics / Software packages and methods / Multi-study correlation or factor analysis

MSFA2over 4 years ago2016 - - De Vito - multi-study factor analysis: same features, different samples -

awesome-multi-omics / Software packages and methods / Multi-omics simulation

InterSIM2016 - - Chalise - methylation, gene expression and protein expression -
MOSim2019 - - Martinez-Mira - RNA-seq, ATAC-seq (DNase-seq), ChIP-seq, small RNA-seq and Methyl-seq. -
OmicsSIMLA2019 - - Chung - DNA, CNV, WGBS, RNAseq, Protein expression -

awesome-multi-omics / Multi-omics reviews / evaluations

Multivariate data analysis: The French way2008 - Holmes -
A practical data processing workflow for multi-OMICS projects2014 - Kohl -
Measuring multivariate association and beyond2016 - Josse -
Multi-omic data integration enables discovery of hidden biological regularities2016 - Ebrahim -
Dimension reduction techniques for the integrative analysis of multi-omics data2016 - Meng -
A review on machine learning principles for multi-view biological data integration2016 - Li -
More Is Better: Recent Progress in Multi-Omics Data Integration Methods2017 - Huang -
Multi-omics approaches to disease2017 - Hasin -
Statistical data integration: Challenges and opportunities2017 - Allen -
Multi-omic and multi-view clustering algorithms: review and cancer benchmark2018 - Rappoport -
Current multiblock methods: Competition or complementarity? A comparative study in a unified framework2018 - Bougeard -
Integrative omics for health and disease2018 - Karczewski -
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data2018 - Yan -
Integrated omics: tools, advances and future approaches2019 - Misra -
Evaluation of integrative clustering methods for the analysis of multi-omics data2019 - Chauvel -
Consistency and overfitting of multi-omics methods on experimental data2019 - McCabe - -
Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration2019 - Pierre-Jean -
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community2019 - Pinu -
A Selective Review of Multi-Level Omics Data Integration Using Variable Selection2019 - Wu -
Multitable methods for microbiome data integration2019 - Sankaran - -
Heterogeneous Multi-Layered Network Model for Omics Data Integration and Analysis2020 - Lee -
Large-scale benchmark study of survival prediction methods using multi-omics data2020 - Herrmann - -
Multiview learning for understanding functional multiomics2020 - Nguyen -
Metabolomics and multi-omics integration: a survey of computational methods and resources2020 - Eicher -
Benchmarking joint multi-omics dimensionality reduction approaches for cancer study2020 - Cantini -
Multi-omics Data Integration, Interpretation, and Its Application2020 - Subramanian -
State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing2020 - Krassowski - -
Data-Driven Modeling of Pregnancy-Related Complications2021 - Espinosa -
Uncovering Cross-Cohort Molecular Features with Multi-Omics Integration Analysis2022 - Jiang -
Machine learning for multi-omics data integration in cancer2022 - Cai -

awesome-multi-omics / Multi-omics application papers

A multivariate analysis approach to the integration of proteomic and gene expression data2007 - Fagan -
The duality diagram in data analysis: Examples of modern applications2011 - De la Cruz - -
Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data2014 - Tomescu -
A community effort to assess and improve drug sensitivity prediction algorithms2014 - Costello (NCI/DREAM) -
Inferring gene–gene interactions and functional modules using sparse canonical correlation analysis2015 - Wang -
TCGA2STAT: simple TCGA data access for integrated statistical analysis in R2016 - 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 samples2018 - Skelly - -
Comprehensive integration of single cell data2018 - Stuart -
Joint analysis of gene expression levels and histological images identifies genes associated with tissue morphology2018 - Ash -
Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data2019 - Xu -
Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy2019 - Ghaemi - Multi-omics in pregnancy using stacked generalization

awesome-multi-omics / Multi-omics data management

MultiAssayExperiment2017 - - Ramos - Software for the integration of multi-omics experiments in Bioconductor -
muon222over 1 year ago2021 - - Bredikhin -

awesome-multi-omics / Batch effect correction

MultiBaC5over 4 years ago2020 - - 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 Types2020 - - - June 14-19, 2020 in Banff, Canada

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