{"id":23535174,"url":"https://github.com/warelab/necorr","last_synced_at":"2025-04-23T04:19:57.550Z","repository":{"id":86786282,"uuid":"75867223","full_name":"warelab/NECorr","owner":"warelab","description":null,"archived":false,"fork":false,"pushed_at":"2024-06-18T17:17:45.000Z","size":137722,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-29T22:04:12.524Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/warelab.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2016-12-07T19:08:38.000Z","updated_at":"2024-06-18T17:17:48.000Z","dependencies_parsed_at":"2024-06-18T00:33:22.010Z","dependency_job_id":null,"html_url":"https://github.com/warelab/NECorr","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/warelab%2FNECorr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/warelab%2FNECorr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/warelab%2FNECorr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/warelab%2FNECorr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/warelab","download_url":"https://codeload.github.com/warelab/NECorr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250366975,"owners_count":21418810,"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":"2024-12-26T01:15:23.153Z","updated_at":"2025-04-23T04:19:57.517Z","avatar_url":"https://github.com/warelab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\ntitle: \"Network Correlation Analysis (NECorr)\"\noutput: github_document\n---\n\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(echo = TRUE)\n```\n\n# Contents\n\n-   [Overview](#overview)\n-   [Repo Contents](#repo-contents)\n-   [System Requirements](#system-requirements)\n-   [Installation Guide](#installation-guide)\n-   [Instructions for Use](#instructions-for-use)\n-   [License](./LICENSE)\n-   [Citation](#citation)\n\n# Overview {#overview}\n\nNECorr is a R package based on multiple-criteria decision-making algorithms. With the objective of ranking genes and their interactions in a selected condition or tissue, NECorr uses molecular network topology as well as global transcriptomics analysis to find condition/tissue-specific hub genes and their regulators.\n\n# Repo Contents {#repo-contents}\n\n-   [R](./R): `R` package code.\n-   [man](./man): package manual for help in R session.\n-   [int](./data): test data using dummies datasets and model.\n-   [tests](./tests): `R` test with the data.\n\n# System Requirements {#system-requirements}\n\n## Hardware Requirements\n\nThe package require a long running time depending of the size of molecular network. A computer with 16 GB RAM is recommended to run the package.\nThe necessary C++ or GCC libraries are needed as the software is running partially on Rccp.\n\n## Software Requirements\n\n### OS Requirements\n\nThis package is supported for *Mac OS*, *Windows* and *Linux* operating systems. The package has been tested on the following systems:\n\nLinux: Redhat RHEL 7.4\\\nMac OSX: OS X 11.2.3; and 12.6\n\nThe NECorr packages requires the R version 3.4.2 or higher and a standard computer with enough RAM to support the operations defined by a user. For minimal performance, this will be a computer with about 1 GB of RAM.\n\n### Installing R version 3.5 on Linux\n\nThe latest version of R can be installed as follows on *Linux*:\n\n```{bash eval=FALSE, include=TRUE}\nwget https://cran.rstudio.com/bin/macosx/R-3.4.2.pkg\nsudo installer -pkg R-3.5.2.pkg -target /\n\n```\n\n# Installation Guide {#installation-guide}\n\n## Devtools\nFrom an `R` session, type:\n\n```{r eval=FALSE, include=TRUE}\nrequire(devtools)\ninstall_github('warelab/NECorr', build_vignettes=TRUE, dependencies=TRUE, upgrade_dependencies=TRUE)  \n```\n\nThe package should take approximately 20 seconds to install with vignettes on a recommended computer.\n\n## Package Versions\n\nThe `NECorr` package dependencies will be installed automatically. \nThe following [BioConductor](https://www.bioconductor.org/) package will need to be installed separately\n\n```{r eval=FALSE, include=TRUE}\nBiobase: 2.54.0\nBiocGenerics: 0.40.0\nlimma: 3.50.3 \nAnnotationDbi: 1.56.2\nGenomeInfoDbData: 1.2.7 \nsupraHex: 1.14.0\n```\n\n# Instructions for Use {#instructions-for-use}\n\nPlease see the vignettes for help using the package:\n\n```{r eval=FALSE, include=TRUE}\nvignette(\"Necorr\", package=\"NECorr\")\nvignette(\"gini\", package=\"NECorr\")\n```\n\n# Citation {#citation}\n\nFor citing code or the paper, please use [this citation](https://www.biorxiv.org/content/early/2018/05/21/326868).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwarelab%2Fnecorr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwarelab%2Fnecorr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwarelab%2Fnecorr/lists"}