{"repo":"saezlab/cosmosR","free":true,"listed":false,"github":"https://github.com/saezlab/cosmosR","clone":"git clone https://github.com/saezlab/cosmosR.git","description":"COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.","language":"R","stars":70,"topics":["metabolomic-data","proteomics","phosphoproteomics","data-integration","transcriptomics","network-modelling"],"license":"GPL-3.0","category":"data-pipelines","readme_excerpt":"cosmosR Overview COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets. COSMOS leverages extensive prior knowledge of signaling pathways, metabolic networks, and gene regulation with computational methods to estimate activities of transcription factors and kinases as well as network-level causal reasoning. This pipeline can provide mechanistic explanations for experimental observations across multiple omic data sets. COSMOS finds coherent subnetwork causally connecting as many deregulated TFs, kinases/phosphatases and metabolites as possible. The subnetwork is extracted from a novel integrated PKN (available here) spanning signaling, transcriptional regulation and metabolism. Transcription factors activities are inferred from gene expression with decoupleR. Kinase activities are inferred from phosphoproteomic with a kinase/substrate network of Omnipath, a meta resource of protein-protein. The scripts to generate the current network can be found here: https://github.com/saezlab/meta PKN BIGG. You can also use COSMOS if you don't have metabolomic data, to connect TF activities (from transcriptomic) with kinase activities (from phosphoproteomic) for exmaple ! Installation R = 4.1 is required If you don't have R 4.1, you can also clone the github repository on your machine, create a new R project with R studio from the cosmosR folder, change the R version to your own R version in the DESCRIPT","default_branch":null,"files":null,"tree":[],"storefront":"/r/saezlab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/saezlab/cosmosR/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."}