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Multi-Omics

General Resources for Multi-Omics

Contents

Tools

  • PMA - Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis, described in Witten, Tibshirani and Hastie (2009) doi:10.1093/biostatistics/kxp008 and Witten and Tibshirani (2009) Extensions of sparse canonical correlation analysis, with applications to genomic data doi:10.2202/1544-6115.1470.
  • gesca - Hwang - RGSCA regularized generalized structured component analysis
  • RGCCA - Tenenhaus - Regularized Generalized CCA and Sparse Generalized CCA
  • scca - Lee - Sparse Canonical Covariance Analysis for High-throughput Data
  • STATIS/DiSTATIS - Abdi - structuring three-way statistical tables
  • RIMBANET - Zhu - Reconstructing Integrative Molecular Bayesian Networks
  • FactoMineR - Abdi - MFA: multiple factor analysis
  • JIVE - Lock - joint & individual variance explained
  • pandaR - Schlauch - Passing Attributes between Networks for Data Assimilation
  • omicade4 - Meng - MCIA: multiple co-interia analysis
  • STATegRa - Planell - DISCO, JIVE, & O2PLS
  • GFAsparse - Khan - group factor analysis sparse
  • CCAGFA - Klami - Bayesian Canonical Correlation Analysis and Group Factor Analysis
  • CMF - Klami - collective matrix factorization
  • moGSA - Meng - multi-omics gene set analysis
  • iNMF - Yang - integrative NMF
  • BASS - Zhao - Bayesian group factor analysis
  • imputeMFA in missMDA - Voillet - multiple imputation for multiple factor analysis (MI-MFA)
  • PLSCA - Beaton - Partial Least Square Correspondence Analysis
  • mixOmics - Rohart - various methods
  • mixedCCA - Yoon - sparse CCA for data of mixed types
  • SLIDE - Gaynanova - Structural Learning and Integrative Decomposition of Multi-View Data
  • fCCAC - Madrigal - functional canonical correlation analysis to evaluate covariance
  • TSKCCA - Yoshida - Sparse kernel canonical correlation analysis
  • AJIVE - Feng - angle-based JIVE
  • MOFA - Argelaguet - multi-omics factor analysis
  • PCA+CCA - Brown
  • JACA - Zhang - Joint Association and Classification Analysis
  • pCIA - Min - penalized COI
  • OmicsPLS - Bouhaddani - O2PLS implemented in R, with an alternative cross-validation scheme
  • SCCA-BC - Pimentel - Biclustering by sparse canonical correlation analysis
  • WON-PARAFAC - Kim - weighted orthogonal nonnegative parallel factor analysis
  • BIDIFAC - Park - bidimensional integrative factorization
  • SmCCNet - Shi - sparse multiple canonical correlation network analysis
  • msPLS - Csala - multiset sparse partial least squares path modeling
  • D-CCA - Shu - Decomposition-based Canonical Correlation Analysis
  • COMBI - Hawinkel - Compositional Omics Model-Based Integration
  • DPCCA - Gundersen - Deep Probabilistic CCA
  • MEFISTO - Velten - spatial or temporal relationships
  • MultiPower - Tarazona - Sample size in multi-omic experiments
  • mixedCCA - Yoon - Sparse semiparametric CCA for data of mixed types
  • ade4 - Dray - Implementing the Duality Diagram for Ecologists
  • THEME - Verron - THEmatic Model Exploration
  • iCluster - Shen
  • MDI - Kirk
  • iClusterPlus - Mo
  • BCC - Lock - Bayesian consensus clustering
  • iBAG - Wang - Integrative Bayesian Analysis of Genomics
  • SNF - Wang
  • clusternomics - Gabasova
  • IBOOST - Wong
  • Spectrum - John
  • INF - Chierici and Bussola
  • maui - Ronen - Stacked VAE + clustering predictive of survival
  • IntegrativeVAEs - Simidjievski - Variational autoencoders + classification
  • DeepProg - Poirion - DL and ML ensemble + survival prediction
  • SHAE - Wissel - Supervised Hierarchical Autoencoder + survival prediction
  • MolTi-DREAM - Didier - identifying communities from multiplex networks, and annotated the obtained clusters
  • RWR-MH - Valdeolivas - Random walk with restart on multiplex and heterogeneous biological networks
  • MOGAMUN - Novoa-del-toro - A multi-objective genetic algorithm to find active modules in multiplex biological networks
  • RWRF - Wen - Random Walk with Restart for multi-dimensional data Fusion
  • cardelino - - gene expression states to clones (SNVs from scRNA-seq + bulk exome data)
  • clonealign - Campbell - gene expression states to clones (scRNA-seq + scDNA-seq (CNV))
  • CiteFuse - Kim - CITE-seq data analysis
  • CoSpar - Wang - infer dynamics by integrating state and lineage information
  • MSFA - De Vito - multi-study factor analysis: same features, different samples