{"repo":"Trhova/Multi-omics","free":true,"listed":false,"github":"https://github.com/Trhova/Multi-omics","clone":"git clone https://github.com/Trhova/Multi-omics.git","description":"Intuitive guide to multi-omics integration with toy examples: supervised latent components (DIABLO), unsupervised shared/partial/unique structure (DIVAS), VAEs/conditional VAEs, and key baselines (MOFA, JIVE, SNF) with practical tips + code.","language":"Python","stars":92,"topics":["data-integration","diablo","latent-variables","multiomics","variational-autoencoder","bioinformatics","machine-learning","microbiome"],"license":null,"category":"machine-learning","readme_excerpt":"Practical Multi-Omics Integration (DIABLO, DIVAS, VAEs + a few essentials) A condensed-but-thorough, intuitive guide for people doing multi-omics (microbiome, metabolomics, transcriptomics, proteomics…) who want to integrate layers without pretending correlation = causation . This repo covers: - DIABLO (supervised multi-omics components + feature selection) - DIVAS (shared-by-all vs shared-by-some vs unique structure) - Variational Autoencoders (VAEs) for multi-omics embeddings and reconstruction (including label-conditioning) - Related method families: MOFA , JIVE , SNF , iCluster , and baselines like CCA / PLS / PCA We use one consistent toy example throughout (4 patients, 3 omics blocks, 1 group label) and define every term as we go. Quickstart Python: - Inspect toy data: python python/01 make toy data.py - Early integration baseline (concat + PCA): python python/03 baseline concat pca.py - Two-block baseline (microbiome ↔ metabolomics CCA): python python/04 baseline cca microbe met.py - Multi-omics latent demo (linear baseline; optional VAE with torch): python python/02 multimodal vae skeleton.py Optional uv venv (nice for VS Code): - ./scripts/uv env.sh install-uv - ./scripts/uv env.sh venv - ./scripts/uv env.sh run python/03 baseline concat pca.py R: - Inspect toy data: Rscript r/01 make toy data.R - DIABLO mechanics demo: Rscript r/02 diablo mixomics example.R (requires mixOmics ) Table of contents - 0) Big picture: what integration can (and can't) do - 1) The toy exam","default_branch":null,"files":null,"tree":[],"storefront":"/r/Trhova","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/Trhova/Multi-omics/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}