{"id":19630514,"url":"https://github.com/mahshaaban/mircancerdb","last_synced_at":"2025-04-28T06:31:54.608Z","repository":{"id":185878350,"uuid":"102078270","full_name":"MahShaaban/miRCancerdb","owner":"MahShaaban","description":"A database for microRNA-gene/protein expression correlation in cancer.","archived":false,"fork":false,"pushed_at":"2017-11-07T02:27:40.000Z","size":1438,"stargazers_count":9,"open_issues_count":0,"forks_count":5,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-10-26T05:15:54.938Z","etag":null,"topics":["cancer-genomics","database","microrna","r","sqlite","tcga-data"],"latest_commit_sha":null,"homepage":"https://mahshaaban.shinyapps.io/miRCancerdb/","language":"R","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/MahShaaban.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}},"created_at":"2017-09-01T05:50:47.000Z","updated_at":"2023-06-06T19:54:11.000Z","dependencies_parsed_at":null,"dependency_job_id":"a5279d49-8d43-40f9-9c94-f7a892c64995","html_url":"https://github.com/MahShaaban/miRCancerdb","commit_stats":null,"previous_names":["mahshaaban/mircancerdb"],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MahShaaban%2FmiRCancerdb","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MahShaaban%2FmiRCancerdb/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MahShaaban%2FmiRCancerdb/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MahShaaban%2FmiRCancerdb/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MahShaaban","download_url":"https://codeload.github.com/MahShaaban/miRCancerdb/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224099608,"owners_count":17255578,"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":["cancer-genomics","database","microrna","r","sqlite","tcga-data"],"created_at":"2024-11-11T12:02:43.262Z","updated_at":"2024-11-11T12:02:44.475Z","avatar_url":"https://github.com/MahShaaban.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"![version](https://img.shields.io/badge/version-v1.0-blue.svg)\n[![status](https://img.shields.io/badge/shinyapps.io-running-green.svg)](https://mahshaaban.shinyapps.io/miRCancerdb/)  \n\n# miRCancerdb  \nA database for microRNA-gene/protein correlation in cancer.  \nA web interactive interface for this database is available [here](https://mahshaaban.shinyapps.io/miRCancerdb/)  \nA compressed built database file is available here [here](https://figshare.com/articles/miRCancer_db_gz/5576329)\n\n# Overview  \nmiRCancerdb is database of expression correlation of expression of microRNAs and genes/proteins.\nThe web interface provides an easy access to the database without having to write any code.\nAmong other features, users can search, choose, visualize and downlaod the particular subsets of the data.  \n\n# Datasets  \nThe expression data was obtained from The Cancer Genome Atlas [(TCGA)](https://tcga-data.nci.nih.gov) using [RTCGA](http://bioconductor.org/packages/release/bioc/html/RTCGA.html) R package.\nAnd the targets data were obtained form [TargetScan](http://www.targetscan.org) using [targetscan.Hs.eg.db](http://www.bioconductor.org/packages/devel/data/annotation/html/targetscan.Hs.eg.db.html) [Bioconductor](http://bioconductor.org) package.  \n\n# Workflow\n[(TCGA)](https://tcga-data.nci.nih.gov) expression data for microRNAs, mRNA and proteins were obtained using [RTCGA](http://bioconductor.org/packages/release/bioc/html/RTCGA.html) R package. \nThe expression correlation were calculated for each microRNA to each feature; gene/protein in each [(TCGA)](https://tcga-data.nci.nih.gov) study.\nAn SQLite database were build using these corelations. In addition, expression profiles of each miroRNA and\nmicroRNA targets data were obtained from [targetscan.Hs.eg.db](http://www.bioconductor.org/packages/devel/data/annotation/html/targetscan.Hs.eg.db.html) [Bioconductor](http://bioconductor.org) package and added to the database.\n\n# Installation  \nA collection of funtions needed to build the database is provided as an R package called `sqlome`. The package is available on github and can be installed using:\n\n```r\ndevtools::install_github('MahShaaban/sqlome')\n```\n\nClone or download this repository, navigate to the miRCancerdb directory and run make to build the database from scratch and\nlaunch a shiny browser application. \n\n```\ngit clone https://github.com/MahShaaban/miRCancerdb\ncd miRCancerdb\nmake\n```\n\nIndeed, the same can be achieved through Rstudio and the sqlite db file can be accessed using DBI library in R.\n\n## More  \nCitation: \u003cmanuscript\u003e  \nUsign cRegulome: https://github.com/MahShaaban/cRegulome  \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmahshaaban%2Fmircancerdb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmahshaaban%2Fmircancerdb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmahshaaban%2Fmircancerdb/lists"}