Package: isn-tractor
ISN-tractorInteractome based Individual Specific Networks (Ib-ISN)About the project: Interactome Based Individual Specific Networks (Ib-ISN) Computation and its relevanceAnindividual-specific networkin biology is a sort of network that depicts the relationships between the genes, proteins, or other biological molecules of a particular individual.It is sometimes referred to as a "personalised network" or "individual network".These networks can be computed using a range of data types, including genetic information, details on protein expression, and other omics data.One of the top aims of individual-specific networks is to comprehendhow interactions between different biological molecules affect an individual's overall function and behaviour. For example, an individual-specific network can be used to identify the proteins that are essential for maintaining a certain biological activity or the critical regulatory networks that control a person's gene expression. It is also possible to forecast how genetic or environmental changes may affect a person's biology by using individual-specific networks. For instance, they can be used to foretell how a specific mutation or environmental exposure may impact the way a certain gene or pathway functions.The entire range of interactions between biological macromolecules in a cell, including as those mediated by protein-ligand binding or solely functional connections between proteins, are referred to as theinteractome. As a result, it offers a summary of the functional activity within a particular cell. Extracellular protein-protein interaction (PPI) networks are particularly significant to illness causation, diagnosis, and treatment due to a number of features. Their functional diversity, chaos, and complexity are a few of these.Luck et al.introducedHuRI, a human "all-by-all" reference interactome map of human binary protein interactions, which has been demonstrated to have over 53,000 protein-protein interactions.HuRI, asa systematic proteome-wide reference that connects genetic variation to phenotypic outcomes,was the impetus for our decision to create a novel approach for computing interactome-based ISN, starting from SNP data and ending with a gene-based network.Getting startedInstallationpipinstallisn-tractorUsageData preprocessing and imputationimportpandasaspdimportisn_tractor.ibisnasitsnps=pd.read_csv("snp_dataset.csv")snp_meta=pd.read_csv("snp_metadata.csv")interact=pd.read_csv("interactome_interactions.csv")gtf=pd.read_csv("human_genes.csv")# returnsgene_info=it.preprocess_gtf(gtf)# returnsit.preprocess_snp(snp_meta)# returnssnps=it.impute(snps)Mapping# returnsit.positional_mapping(snp_meta,gene_info,neighborhood=5)Features mapping and interaction# returns(interact_snp,interact_gene)=it.snp_interaction(interact,gene_info,snp_info)Individual Specific Network (ISN) computationisn=it.compute_isn(df,interact_snp,interact_gene,"spearman","max")For more examples, please refer to theDocumentation.RoadmapComplete theUsagesectionAdd documentation with examplesConsider a new function for functional mappingAdd:Imputation with file savingFunctionisn_calculation_per_edgeProgressbarContributingContributions are what make the open source community such a wonderful place to learn, be inspired, and create.
Your contributions will be greatly appreciated.If you have an idea for how to improve this, please fork the repository and submit a pull request. You can alternatively open a new issue with the tag "improvement". Don't forget to :star: the project! Thank you once more!Fork the ProjectCreate your Feature Branch(git checkout -b feature/AmazingFeature)Commit your Changes(git commit -m 'Add some AmazingFeature')Push to the Branch(git push origin feature/AmazingFeature)Open a Pull RequestLicenseContactGiada Lalli -giada.lalli@kuleuven.beZuqi Li -zuqi.li@kuleuven.beFederico Melograna -federico.melograna@kuleuven.beProject Link:Acknowledgments