{"id":24529045,"url":"https://github.com/saezlab/gene-network-inference-in-r","last_synced_at":"2026-01-02T06:54:55.799Z","repository":{"id":77872674,"uuid":"333537768","full_name":"saezlab/gene-network-inference-in-R","owner":"saezlab","description":"Mutual information-based and bicor-based methods for genome-wide reverse engineering of gene regulatory networks in R.","archived":false,"fork":false,"pushed_at":"2021-04-04T18:41:11.000Z","size":12893,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-01-22T07:37:41.204Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-01-27T19:32:22.000Z","updated_at":"2022-05-27T00:44:10.000Z","dependencies_parsed_at":"2023-03-05T13:45:22.111Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/gene-network-inference-in-R","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgene-network-inference-in-R","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgene-network-inference-in-R/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgene-network-inference-in-R/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fgene-network-inference-in-R/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/gene-network-inference-in-R/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243769947,"owners_count":20345215,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-01-22T07:34:33.090Z","updated_at":"2026-01-02T06:54:55.772Z","avatar_url":"https://github.com/saezlab.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"## Overview\n\n\n**net_inf_ARACNE.Rmd** and **net_inf_WGCNA.Rmd** scripts provide mutual information-based and bicor-based methods for the genome-wide reverse engineering of gene regulatory networks, implemented in [Minet R package](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-461), and [WGCNA R package](https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/), respectively. Here, we use [ARACNE](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-S1-S7) and [WGCNA](https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/) to infer a gene regulatory network from a [data set](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119931) of 27123 genes and 6 samples. For further details about pre-processing steps (normalization and noise elimination), please refer to https://github.com/saezlab/transcriptutorial/blob/master/scripts/01_normalisation.md.\n\nThe **dorothea_int_aracne.Rmd** script is used to extract matching TF-Target ineractions between [Dorothea](https://bioconductor.org/packages/release/data/experiment/html/dorothea.html) and [ARACNE](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-S1-S7) inferred regulons.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fgene-network-inference-in-r","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fgene-network-inference-in-r","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fgene-network-inference-in-r/lists"}