├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE └── README.md /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Covenant Code of Conduct 2 | 3 | ## Our Pledge 4 | 5 | In the interest of fostering an open and welcoming environment, we as contributors pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. 6 | 7 | ## Our Standards 8 | 9 | Examples of behavior that contributes to creating a positive environment include: 10 | 11 | * Using welcoming and inclusive language 12 | * Being respectful of differing viewpoints and experiences 13 | * Gracefully accepting constructive criticism 14 | * Focusing on what is best for the community 15 | * Showing empathy towards other community members 16 | 17 | Examples of unacceptable behavior by participants include: 18 | 19 | * The use of sexualized language or imagery and unwelcome sexual attention or advances 20 | * Trolling, insulting/derogatory comments, and personal or political attacks 21 | * Public or private harassment 22 | * Publishing others' private information, such as a physical or electronic address, without explicit permission 23 | * Other conduct which could reasonably be considered inappropriate in a professional setting 24 | 25 | ## Our Responsibilities 26 | 27 | Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. 28 | 29 | Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. 30 | 31 | ## Scope 32 | 33 | This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. 34 | 35 | ## Enforcement 36 | 37 | Instances of abusive, harassing, or otherwise unacceptable behavior 38 | may be reported by contacting the project team at 39 | `michaelisaiahlove at gmail dot com`. 40 | The project team will review and investigate all 41 | complaints, and will respond in a way that it deems appropriate to the 42 | circumstances. The project team is obligated to maintain 43 | confidentiality with regard to the reporter of an incident. Further 44 | details of specific enforcement policies may be posted separately. 45 | 46 | Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. 47 | 48 | ## Attribution 49 | 50 | This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version] 51 | 52 | [homepage]: http://contributor-covenant.org 53 | [version]: http://contributor-covenant.org/version/1/4/ 54 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | Contribution and suggestions are welcome! Simply 2 | 3 | 1. [Fork this repository](https://help.github.com/articles/fork-a-repo/) 4 | 2. Make a change to `README.md` 5 | 3. [Submit a pull request](https://help.github.com/articles/creating-a-pull-request/). 6 | 7 | Please ensure your pull request adheres to the following guidelines: 8 | 9 | - Please search previous suggestions before making a new one, as yours 10 | may be a duplicate. 11 | - Use the following format: YEAR - `[resource](link to software)` - first author's last name - very short description - `[paper](link to DOI, PMC, or arxiv)`. 12 | - **For avoiding future dead links, please restrict links to DOI, PMC or arxiv when possible** 13 | - For YEAR, use either the date of the publication, or if not yet 14 | published, the date of the preprint / software release. 15 | - Order projects chronologically within each category. 16 | - If adding a description at all, keep it < 6 words. 17 | - Check your spelling and grammar. 18 | - New categories, or improvements to the existing categorization are welcome. 19 | 20 | Thank you for your suggestions! 21 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 Mike Love 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # awesome-multi-omics 2 | 3 | A [community-maintained](https://github.com/mikelove/awesome-multi-omics/graphs/contributors) list of software packages for multi-omics data analysis. 4 | 5 | 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: 6 | 7 | * multi-modal 8 | * multi-table 9 | * multi-way 10 | 11 | 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. 12 | 13 | The repo is in the style of Sean Davis' 14 | [awesome-single-cell](https://github.com/seandavi/awesome-single-cell) 15 | repo for single-cell analysis methods. 16 | 17 | [Contributions welcome](https://github.com/mikelove/awesome-multi-omics/blob/master/CONTRIBUTING.md)... 18 | 19 | For brevity, below lists only the first author of multi-omics methods. 20 | 21 | ## Software packages and methods 22 | 23 | ### Multi-omics correlation or factor analysis 24 | 25 | - 2007 - **SCCA** - Parkhomenko - sparse CCA - [paper 1](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367499/), [paper 2](https://doi.org/10.2202/1544-6115.1406) 26 | - 2008 - **PCCA** - Waaijenborg - penalized CCA / CCA-EN - [paper](https://doi.org/10.2202/1544-6115.1329) 27 | - 2009 - [PMA](https://CRAN.r-project.org/package=PMA) - Witten - Sparse Multi CCA - [paper 1](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697346/), [paper 2](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861323/) 28 | - 2009 - **sPLS** - Lê Cao - sparse PLS - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640358/) 29 | - 2009 - [gesca](https://CRAN.r-project.org/package=gesca) - Hwang - RGSCA regularized generalized structured component analysis - [paper](https://doi.org/10.1007/s11336-009-9119-y) 30 | - 2010 - **Regularized dual CCA** - Soneson - [paper](https://doi.org/10.1186/1471-2105-11-191) 31 | - 2011 - [RGCCA](https://cran.r-project.org/package=RGCCA) - Tenenhaus - Regularized Generalized CCA and Sparse Generalized CCA - [paper 1](https://www.ncbi.nlm.nih.gov/pubmed/28536930), [paper 2](https://www.ncbi.nlm.nih.gov/pubmed/24550197) 32 | - 2011 - **SNMNMF** - Zhang - Sparse Network-regularized Multiple Non-negative Matrix Factorization - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117336/) 33 | - 2011 - [scca](https://github.com/tomwhoooo/scca_3.0) - Lee - Sparse Canonical Covariance Analysis for High-throughput Data - [paper](https://doi.org/10.2202/1544-6115.1638) 34 | - 2012 - [STATIS/DiSTATIS](https://github.com/HerveAbdi/DistatisR) - Abdi - structuring three-way statistical tables - [paper](https://doi.org/10.1002/wics.198) 35 | - 2012 - **joint NMF** - Zhang - extension of NMF to multiple datasets - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479191/) 36 | - 2012 - **sMBPLS** - Li - sparse MultiBlock Partial Least Squares - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463121/) 37 | - 2012 - **Bayesian group factor analysis** - Virtanen - [paper](http://proceedings.mlr.press/v22/virtanen12.html) 38 | - 2012 - [RIMBANET](http://research.mssm.edu/integrative-network-biology/RIMBANET/RIMBANET_overview.html) - Zhu - Reconstructing Integrative Molecular Bayesian Networks - [paper](https://doi.org/10.1371/journal.pbio.1001301) 39 | - 2013 - [FactoMineR](https://cran.r-project.org/package=FactoMineR) - Abdi - MFA: multiple factor analysis - [paper](https://doi.org/10.1002/wics.1246) 40 | - 2013 - [JIVE](https://genome.unc.edu/jive/) - Lock - joint & individual variance explained - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3671601/) 41 | - 2013 - [pandaR](https://bioconductor.org/packages/release/bioc/html/pandaR.html) - Schlauch - Passing Attributes between Networks for Data Assimilation - [paper](https://doi.org/10.1093/bioinformatics/btx139) 42 | - 2014 - [omicade4](https://bioconductor.org/packages/omicade4) - Meng - MCIA: multiple co-interia analysis - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053266/) 43 | - 2014 - [STATegRa](https://bioconductor.org/packages/STATegRa) - Planell - DISCO, JIVE, & O2PLS - [paper](https://doi.org/10.3389/fgene.2021.620453) 44 | - 2014 - **Joint factor model** - Ray - [paper](https://doi.org/10.1093/bioinformatics/btu064) 45 | - 2014 - [GFAsparse](https://research.cs.aalto.fi/pml/software/GFAsparse/) - Khan - group factor analysis sparse [paper 1](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147909/), [paper 2](https://doi.org/10.1093/bioinformatics/btw207) 46 | - 2015 - **Sparse CCA** - Gao (3rd paper first author is Chen) - [paper 1](https://doi.org/10.1214/15-AOS1332), [paper 2](https://doi.org/10.1214/16-AOS1519), [paper 3](https://arxiv.org/abs/1311.6186) 47 | - 2015 - [CCAGFA](https://cran.r-project.org/package=CCAGFA) - Klami - Bayesian Canonical Correlation Analysis and Group Factor Analysis - [paper 1](https://doi.org/10.1109/TNNLS.2014.2376974), [paper 2](http://www.jmlr.org/papers/v18/16-509.html) 48 | - 2016 - [CMF](https://cran.r-project.org/package=CMF) - Klami - collective matrix factorization - [paper](https://arxiv.org/abs/1312.5921) 49 | - 2016 - [moGSA](https://bioconductor.org/packages/mogsa) - Meng - multi-omics gene set analysis - [paper](https://doi.org/10.1101/046904) 50 | - 2016 - [iNMF](https://github.com/yangzi4/iNMF) - Yang - integrative NMF - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/26377073/) 51 | - 2016 - [BASS](https://github.com/judyboon/BASS) - Zhao - Bayesian group factor analysis - [paper](https://arxiv.org/abs/1411.2698) 52 | - 2016 - `imputeMFA` in [missMDA](https://cran.r-project.org/web/packages/missMDA/index.html) - Voillet - multiple imputation for multiple factor analysis (MI-MFA) - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048483/) 53 | - 2016 - [PLSCA](https://github.com/derekbeaton/PLSCA_Framework) - Beaton - Partial Least Square Correspondence Analysis - [paper](https://doi.org/10.1037/met0000053) 54 | - 2017 - [mixOmics](https://bioconductor.org/packages/mixOmics) - Rohart - various methods - [paper1](https://doi.org/10.1371/journal.pcbi.1005752), [paper2](https://doi.org/10.1093/bioinformatics/bty1054) 55 | - 2017 - [mixedCCA](https://github.com/irinagain/mixedCCA) - Yoon - sparse CCA for data of mixed types - [paper](https://arxiv.org/abs/1807.05274) 56 | - 2017 - [SLIDE](https://github.com/irinagain/SLIDE_Rpackage) - Gaynanova - Structural Learning and Integrative Decomposition of Multi-View Data - [paper](https://arxiv.org/abs/1707.06573) 57 | - 2017 - [fCCAC](https://github.com/pmb59/fCCAC/) - Madrigal - functional canonical correlation analysis to evaluate covariance - [paper](https://doi.org/10.1093/bioinformatics/btw724) 58 | - 2017 - [TSKCCA](https://github.com/kosyoshida/TSKCCA) - Yoshida - Sparse kernel canonical correlation analysis - [paper](https://doi.org/10.1186/s12859-017-1543-x) 59 | - 2017 - **SMSMA** - Kawaguchi - Supervised multiblock sparse multivariable analysis - [paper](https://doi.org/10.1093/biostatistics/kxx011) 60 | - 2018 - [AJIVE](https://github.com/idc9/r_jive) - Feng - angle-based JIVE - [paper](https://arxiv.org/abs/1704.02060) 61 | - 2018 - [MOFA](https://github.com/bioFAM/MOFA) - Argelaguet - multi-omics factor analysis - [paper 1](https://doi.org/10.15252/msb.20178124), [paper 2](https://www.biorxiv.org/content/10.1101/837104v1), [application](https://doi.org/10.1101/519207) 62 | - 2018 - [PCA+CCA](https://github.com/pachterlab/PCACCA/) - Brown - [paper](https://doi.org/10.1371/journal.pgen.1007841) 63 | - 2018 - [JACA](https://github.com/Pennisetum/JACA) - Zhang - Joint Association and Classification Analysis - [paper](https://arxiv.org/abs/1811.08511) 64 | - 2018 - **iPCA** - Tang - Integrated Principal Components Analysis - [paper](https://arxiv.org/abs/1810.00832) 65 | - 2018 - [pCIA](https://www.med.upenn.edu/long-lab/software.html) - Min - penalized COI - [paper](https://www.ncbi.nlm.nih.gov/pubmed/30165424) 66 | - 2018 - **sSCCA** - Safo - structured sparse CCA - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677597/) 67 | - 2018 - **SWCCA** - Min - Sparse Weighted CCA - [paper](https://arxiv.org/abs/1710.04792) 68 | - 2018 - [OmicsPLS](https://github.com/selbouhaddani/OmicsPLS) - Bouhaddani - O2PLS implemented in R, with an alternative cross-validation scheme - [paper](https://doi.org/10.1186/s12859-018-2371-3) 69 | - 2018 - [SCCA-BC](https://github.com/pimentel/scca-bc) - Pimentel - Biclustering by sparse canonical correlation analysis - [paper](https://doi.org/10.1007/s40484-017-0127-0) 70 | - 2018 - [mixKernel](https://cran.r-project.org/package=mixKernel) - Mariette - kernel method for unsupervised multi-omics integration - [paper 1](http://dx.doi.org/10.1093/bioinformatics/btx682), [paper 2](http://dx.doi.org/10.1093/nargab/lqac014) 71 | - 2019 - [WON-PARAFAC](https://github.com/NKI-CCB/won-parafac) - Kim - weighted orthogonal nonnegative parallel factor analysis - [paper](https://doi.org/10.1038/s41467-019-13027-2) 72 | - 2019 - [BIDIFAC](https://github.com/lockEF/bidifac) - Park - bidimensional integrative factorization - [paper 1](https://doi.org/10.1111/biom.13141), [paper 2](https://arxiv.org/abs/2002.02601) 73 | - 2019 - [SmCCNet](https://cran.r-project.org/web/packages/SmCCNet/index.html) - Shi - sparse multiple canonical correlation network analysis - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6931269/) 74 | - 2020 - [msPLS](https://github.com/acsala/sPLSPM) - Csala - multiset sparse partial least squares path modeling - [paper](https://doi.org/10.1186/s12859-019-3286-3) 75 | - 2020 - **MOTA** - Fan - network-based multi-omic data integration for biomarker discovery - [paper](https://doi.org/10.3390/metabo10040144) 76 | - 2020 - [D-CCA](https://github.com/shu-hai/D-CCA) - Shu - Decomposition-based Canonical Correlation Analysis - [paper](https://doi.org/10.1080/01621459.2018.1543599) 77 | - 2020 - [COMBI](https://bioconductor.org/packages/combi) - Hawinkel - Compositional Omics Model-Based Integration - [paper](https://doi.org/10.1093/nargab/lqaa050) 78 | - 2020 - [DPCCA](https://github.com/gwgundersen/dpcca) - Gundersen - Deep Probabilistic CCA - [paper](http://proceedings.mlr.press/v115/gundersen20a.html) 79 | - 2020 - [MEFISTO](https://biofam.github.io/MOFA2/MEFISTO.html) - Velten - spatial or temporal relationships - [preprint](https://doi.org/10.1101/2020.11.03.366674) 80 | - 2020 - [MultiPower](https://github.com/ConesaLab/MultiPower) - Tarazona - Sample size in multi-omic experiments - [paper](https://doi.org/10.1038/s41467-020-16937-8) 81 | - 2020 - [mixedCCA](https://cran.r-project.org/web/packages/mixedCCA/) - Yoon - Sparse semiparametric CCA for data of mixed types - [paper](https://doi.org/10.1093/biomet/asaa007) 82 | - 2020 - [smCIA/ssmCIA](https://www.med.upenn.edu/long-lab/software.html) - Min - Sparse (structured sparse) multiple co-Inertia analysis - [paper](https://doi.org/10.1186/s12859-020-3455-4) 83 | - 2023 - [MuVI](https://github.com/MLO-lab/MuVI) - Qoku - Integrate noisy feature sets - [paper](https://arxiv.org/abs/2204.06242) 84 | 85 | ### Ecology multi-table literature 86 | 87 | - 1994 - **COI** - Doledec - Co‐inertia analysis - [paper](https://doi.org/10.1111/j.1365-2427.1994.tb01741.x) 88 | - 2007 - [ade4](https://CRAN.r-project.org/package=ade4) - Dray - Implementing the Duality Diagram for Ecologists - [paper](http://dx.doi.org/10.18637/jss.v022.i04) 89 | 90 | ### Chemometrics multi-table literature 91 | 92 | - 1987 - - Wold - Multi‐way principal components‐and PLS‐analysis - [paper](https://doi.org/10.1002/cem.1180010107) 93 | - 1996 - - Wold - Hierarchical multiblock PLS - [paper](https://doi.org/10.1002/(SICI)1099-128X(199609)10:5/6%3C463::AID-CEM445%3E3.0.CO;2-L) 94 | - 2003 - - Trygg - O2‐PLS, a two‐block (X–Y) latent variable regression (LVR) - [paper](https://doi.org/10.1002/cem.775) 95 | - 2011 - - Hanafi - Connections between multiple COI and consensus PCA - [paper](https://doi.org/10.1016/j.chemolab.2010.05.010) 96 | - 2015 - [THEME](https://github.com/ThomData/R_THEME) - Verron - THEmatic Model Exploration - [paper](https://doi.org/10.1002/cem.2759) 97 | 98 | ### Behavioral research multi-table literature 99 | 100 | - 2013 - DISCO SCA - Schouteden - distinctive and common components with simultaneous-component analysis - [paper 1](https://www.ncbi.nlm.nih.gov/pubmed/23361416), [paper 2](https://www.ncbi.nlm.nih.gov/pubmed/24178130) 101 | 102 | ### Multi-omics clustering / classification / prediction 103 | 104 | *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.* 105 | 106 | - 2009 - [iCluster](https://cran.r-project.org/package=iCluster) - Shen - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800366/) 107 | - 2011 - [PSDF](https://sites.google.com/site/patientspecificdatafusion/home/patientSpecificDataFusion.tar.gz) - Yuan - Data fusion by Bayesian nonparametric Dirichlet modeling - [website](https://sites.google.com/site/patientspecificdatafusion/), [publication](https://doi.org/10.1371/journal.pcbi.1002227) 108 | - 2012 - [MDI](https://warwick.ac.uk/fac/cross_fac/zeeman_institute/zeeman_research/software/) - Kirk - [paper1](https://academic.oup.com/bioinformatics/article/28/24/3290/244641), [paper2](https://www.degruyter.com/document/doi/10.1515/sagmb-2015-0055/html) 109 | - 2013 - [iClusterPlus](https://bioconductor.org/packages/iClusterPlus) - Mo - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600490/) 110 | - 2013 - [BCC](https://github.com/ttriche/bayesCC) - Lock - Bayesian consensus clustering - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789539/) 111 | - 2013 - [iBAG](https://github.com/umich-biostatistics/iBAG) - Wang - Integrative Bayesian Analysis of Genomics - [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546799/) 112 | - 2014 - [SNF](http://compbio.cs.toronto.edu/SNF/SNF/Software.html) - Wang - [paper](https://www.ncbi.nlm.nih.gov/pubmed/24464287) 113 | - 2015 - moCluster - Meng - Derivative of iClusterPlus - [paper](https://doi.org/10.1021/acs.jproteome.5b00824) 114 | - 2017 - [clusternomics](https://cran.r-project.org/web/packages/clusternomics/index.html) - Gabasova - [paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005781) 115 | - 2017 - PFA - Shi - Pattern Fussion analysis - [publication](https://doi.org/10.1093/bioinformatics/btx176) 116 | - 2019 - [IBOOST](http://dlin.web.unc.edu/software/iboost/) - Wong - [paper](https://doi.org/10.1186/s13059-019-1640-4) 117 | - 2019 - [Spectrum](https://cran.r-project.org/web/packages/Spectrum/index.html) - John - [paper](https://doi.org/10.1093/bioinformatics/btz704) 118 | - 2019 - [NEMO](https://github.com/Shamir-Lab/NEMO) - Rappoport - Similarity-based Clustering - [paper](https://doi.org/10.1093/bioinformatics/btz058) 119 | - 2020 - [INF](https://gitlab.fbk.eu/MPBA/INF) - Chierici and Bussola - [paper](https://doi.org/10.1101/2020.04.01.020685) 120 | - 2021 - [ClustOmics](https://github.com/galadrielbriere/ClustOmics) - Brière - Consensus clustering - [paper](https://doi.org/10.1186/s12859-021-04279-1) 121 | - 2021 - [MOGONET](https://github.com/txWang/MOGONET) - Tongxin Wang - Multi-Omics Graph cOnvolutional NETworks - [paper](https://pubmed.ncbi.nlm.nih.gov/34103512/) 122 | 123 | ### Multi-omics autoencoders 124 | 125 | - 2019 - [maui](https://github.com/BIMSBbioinfo/maui) - Ronen - Stacked VAE + clustering predictive of survival - [paper](https://doi.org/10.26508/lsa.201900517) 126 | - 2019 - [IntegrativeVAEs](https://github.com/CancerAI-CL/IntegrativeVAEs) - Simidjievski - Variational autoencoders + classification - [paper](https://doi.org/10.3389/fgene.2019.01205) 127 | - 2019 - [OmiVAE](https://github.com/zhangxiaoyu11/OmiVAE) - Xiaoyu Zhang - Integrated Multi-omics Analysis Using Variational Autoencoders - [paper](https://arxiv.org/abs/1908.06278) 128 | - 2021 - [DeepProg](https://github.com/lanagarmire/DeepProg) - Poirion - DL and ML ensemble + survival prediction - [paper](https://doi.org/10.1186/s13073-021-00930-x) 129 | - 2021 - [SHAE](https://github.com/BoevaLab/Supervised-hierarchical-autoencoders-for-cancer-survival) - Wissel - Supervised Hierarchical Autoencoder + survival prediction - [preprint](https://doi.org/10.1101/2021.09.16.460589) 130 | 131 | ### Multi-omics networks 132 | 133 | - 2018 - [MolTi-DREAM](https://github.com/gilles-didier/MolTi-DREAM/) - Didier - identifying communities from multiplex networks, and annotated the obtained clusters [article](https://dx.doi.org/10.12688%2Ff1000research.15486.2) 134 | - 2018 [NetICS](https://github.com/cbg-ethz/netics) - Christos Dimitrakopoulos - Network-based integration of multi-omics data for prioritizing cancer genes - [paper](https://pubmed.ncbi.nlm.nih.gov/29547932/) 135 | - 2019 - [RWR-MH](https://github.com/alberto-valdeolivas/RWR-MH) - Valdeolivas - Random walk with restart on multiplex and heterogeneous biological networks [article](https://doi.org/10.1093/bioinformatics/bty637) 136 | - 2020 - [MOGAMUN](https://bioconductor.org/packages/MOGAMUN/) - Novoa-del-toro - A multi-objective genetic algorithm to find active modules in multiplex biological networks [preprint](https://www.biorxiv.org/content/10.1101/2020.05.25.114215v1) 137 | - 2021 - [RWRF](https://github.com/Sepstar/RWRF/) - Wen - Random Walk with Restart for multi-dimensional data Fusion [paper](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04029-3) 138 | 139 | ### Single cell multi-omics 140 | 141 | - 2018 - [cardelino](https://github.com/PMBio/cardelino) - - gene expression states to clones (SNVs from scRNA-seq + bulk exome data) - 142 | - 2018 - [clonealign](https://github.com/kieranrcampbell/clonealign) - Campbell - gene expression states to clones (scRNA-seq + scDNA-seq (CNV)) - [paper](https://doi.org/10.1101/344309) 143 | - 2020 - [CiteFuse](https://sydneybiox.github.io/CiteFuse/) - Kim - CITE-seq data analysis [paper](https://doi.org/10.1093/bioinformatics/btaa282) 144 | - 2021 - [CoSpar](https://cospar.readthedocs.io/) - Wang - infer dynamics by integrating state and lineage information - [paper](https://www.biorxiv.org/content/10.1101/2021.05.06.443026v1) 145 | - 2025 - [mLLMCelltype](https://github.com/cafferychen777/mLLMCelltype) - Yang - Multi-model framework for single-cell RNA-seq cell type annotation with uncertainty quantification - [paper](https://doi.org/10.1101/2025.04.10.647852) 146 | 147 | ### Multi-study correlation or factor analysis 148 | 149 | - 2016 - [MSFA](https://github.com/rdevito/MSFA) - De Vito - multi-study factor analysis: same features, different samples - [paper](https://arxiv.org/abs/1611.06350) 150 | 151 | ### Multi-omics simulation 152 | 153 | - 2016 - [InterSIM](https://cran.r-project.org/package=InterSIM) - Chalise - methylation, gene expression and protein expression - [paper](https://dx.doi.org/10.1016%2Fj.cmpb.2016.02.011) 154 | - 2019 - [MOSim](https://bioconductor.org/packages/MOSim) - Martinez-Mira - RNA-seq, ATAC-seq (DNase-seq), ChIP-seq, small RNA-seq and Methyl-seq. - [preprint](http://dx.doi.org/10.1101/421834) 155 | - 2019 - [OmicsSIMLA](https://omicssimla.sourceforge.io/) - Chung - DNA, CNV, WGBS, RNAseq, Protein expression - [paper](https://doi.org/10.1093/gigascience/giz045) 156 | 157 | ## Multi-omics reviews / evaluations 158 | 159 | - 2008 - Holmes - [Multivariate data analysis: The French way](https://projecteuclid.org/euclid.imsc/1207580085) 160 | - 2014 - Kohl - [A practical data processing workflow for multi-OMICS projects](https://doi.org/10.1016/j.bbapap.2013.02.029) 161 | - 2016 - Josse - [Measuring multivariate association and beyond](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658146/) 162 | - 2016 - Ebrahim - [Multi-omic data integration enables discovery of hidden biological regularities](https://doi.org/10.1038/ncomms13091) 163 | - 2016 - Meng - [Dimension reduction techniques for the integrative analysis of multi-omics data](https://doi.org/10.1093/bib/bbv108) 164 | - 2016 - Li - [A review on machine learning principles for multi-view biological data integration](https://doi.org/10.1093/bib/bbw113) 165 | - 2017 - Huang - [More Is Better: Recent Progress in Multi-Omics Data Integration Methods](https://doi.org/10.3389/fgene.2017.00084) 166 | - 2017 - Hasin - [Multi-omics approaches to disease](https://doi.org/10.1186/s13059-017-1215-1) 167 | - 2017 - Allen - [Statistical data integration: Challenges and opportunities](http://www.stat.rice.edu/~gallen/gallen_data_integration_2017.pdf) 168 | - 2018 - Rappoport - [Multi-omic and multi-view clustering algorithms: review and cancer benchmark](https://doi.org/10.1093/nar/gky889) 169 | - 2018 - Bougeard - [Current multiblock methods: Competition or complementarity? A comparative study in a unified framework](https://doi.org/10.1016/j.chemolab.2018.09.003) 170 | - 2018 - Karczewski - [Integrative omics for health and disease](https://doi.org/10.1038/nrg.2018.4) 171 | - 2018 - Yan - [Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data](https://dx.doi.org/10.1093/bib/bbx066) 172 | - 2019 - Misra - [Integrated omics: tools, advances and future approaches](https://doi.org/10.1530/JME-18-0055) 173 | - 2019 - Chauvel - [Evaluation of integrative clustering methods for the analysis of multi-omics data](https://doi.org/10.1093/bib/bbz015) 174 | - 2019 - McCabe - [Consistency and overfitting of multi-omics methods on experimental data](https://doi.org/10.1093/bib/bbz070) - [code](https://github.com/mccabes292/movie) 175 | - 2019 - Pierre-Jean - [Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration](https://doi.org/10.1093/bib/bbz138) 176 | - 2019 - Pinu - [Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community](https://doi.org/10.3390/metabo9040076) 177 | - 2019 - Wu - [A Selective Review of Multi-Level Omics Data Integration Using Variable Selection](https://doi.org/10.3390/ht8010004) 178 | - 2019 - Sankaran - [Multitable methods for microbiome data integration](https://doi.org/10.3389/fgene.2019.00627) - [code](https://github.com/krisrs1128/multitable_review) 179 | - 2020 - Lee - [Heterogeneous Multi-Layered Network Model for Omics Data Integration and Analysis](https://doi.org/10.3389/fgene.2019.01381) 180 | - 2020 - Herrmann - [Large-scale benchmark study of survival prediction methods using multi-omics data](https://arxiv.org/abs/2003.03621) - [code](https://github.com/HerrMo/multi-omics_benchmark_study) 181 | - 2020 - Nguyen - [Multiview learning for understanding functional multiomics](https://doi.org/10.1371/journal.pcbi.1007677) 182 | - 2020 - Eicher - [Metabolomics and multi-omics integration: a survey of computational methods and resources](https://doi.org/10.3390/metabo10050202) 183 | - 2020 - Cantini - [Benchmarking joint multi-omics dimensionality reduction approaches for cancer study](https://www.biorxiv.org/content/10.1101/2020.01.14.905760v1) 184 | - 2020 - Subramanian - [Multi-omics Data Integration, Interpretation, and Its Application](https://dx.doi.org/10.1177/1177932219899051) 185 | - 2020 - Krassowski - [State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing](https://doi.org/10.3389%2Ffgene.2020.610798) - [code](https://github.com/krassowski/multi-omics-state-of-the-field) 186 | - 2021 - Espinosa - [Data-Driven Modeling of Pregnancy-Related Complications](https://doi.org/10.1016/j.molmed.2021.01.007) 187 | - 2022 - Jiang - [Uncovering Cross-Cohort Molecular Features with Multi-Omics Integration Analysis](https://doi.org/10.1101/2022.11.10.515908) 188 | - 2022 - Cai - [Machine learning for multi-omics data integration in cancer](https://doi.org/10.1016/j.isci.2022.103798) 189 | 190 | ## Multi-omics application papers 191 | 192 | - 2007 - Fagan - [A multivariate analysis approach to the integration of proteomic and gene expression data](https://doi.org/10.1002/pmic.200600898) 193 | - 2011 - De la Cruz - [The duality diagram in data analysis: Examples of modern applications](https://doi.org/10.1214/10-AOAS408) - [R notebook](http://lbbe-shiny.univ-lyon1.fr/Reproducible_Research/06-AAS.Thioulouse.2011/) 194 | - 2014 - Tomescu - [Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data](https://doi.org/10.1186/1752-0509-8-S2-S4) 195 | - 2014 - Costello (NCI/DREAM) - [A community effort to assess and improve drug sensitivity prediction algorithms](https://doi.org/10.1038/nbt.2877) 196 | - 2015 - Wang - [Inferring gene–gene interactions and functional modules using sparse canonical correlation analysis](https://doi.org/10.1214/14-AOAS792) 197 | - 2016 - Wan - [TCGA2STAT: simple TCGA data access for integrated statistical analysis in R](https://doi.org/10.1093/bioinformatics/btv677) - [R notebook](http://www.liuzlab.org/TCGA2STAT/) 198 | - 2017 - Butler - [Integrating single-cell transcriptomic data across different conditions, technologies, and species.](https://www.biorxiv.org/content/10.1101/164889v1) 199 | - 2018 - Skelly - [Reference trait analysis reveals correlations between gene expression and quantitative traits in disjoint samples](https://www.biorxiv.org/content/10.1101/489542v1) - [R notebook](https://daskelly.github.io/reference_traits/reference_trait_analysis_walkthrough.html) 200 | - 2018 - Stuart - [Comprehensive integration of single cell data](https://www.biorxiv.org/content/10.1101/460147v1) 201 | - 2018 - Ash - [Joint analysis of gene expression levels and histological images identifies genes associated with tissue morphology](https://doi.org/10.1101/458711) 202 | - 2019 - Xu - [Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data](https://doi.org/10.1186/s12967-019-2010-4) 203 | - 2019 - Ghaemi - [Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy](https://doi.org/10.1093/bioinformatics/bty537) Multi-omics in pregnancy using stacked generalization 204 | 205 | ## Multi-omics data management 206 | 207 | - 2017 - [MultiAssayExperiment](https://bioconductor.org/packages/MultiAssayExperiment/) - Ramos - Software for the integration of multi-omics experiments in Bioconductor - [paper](https://doi.org/10.1158/0008-5472.CAN-17-0344). 208 | - 2021 - [muon](https://github.com/pmbio/muon) - Bredikhin - [Multimodal omics analysis framework](https://doi.org/10.1101/2021.06.01.445670) 209 | 210 | ## Batch effect correction 211 | 212 | - 2020 - [MultiBaC](https://github.com/ConesaLab/MultiBaC) - Ugidos - [MultiBaC: A strategy to remove batch effects between different omic data types](https://doi.org/10.1177/0962280220907365) and [R package publication](https://doi.org/10.1093/bioinformatics/btac132) 213 | - [A multivariate method to correct for batch effects in microbiome data]() 214 | 215 | ## Meetings and workshops 216 | 217 | - 2020 - [Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Types](https://www.birs.ca/events/2020/5-day-workshops/20w5197) - [Hackathon details](https://github.com/BIRSBiointegration/Hackathon) - June 14-19, 2020 in Banff, Canada 218 | --------------------------------------------------------------------------------