{"id":15384672,"url":"https://github.com/bblodfon/sandhu-2015","last_synced_at":"2026-07-18T00:12:22.497Z","repository":{"id":90675316,"uuid":"462325113","full_name":"bblodfon/sandhu-2015","owner":"bblodfon","description":"Reproducing the mRNA and miRNA expression data preprocessing pipeline from Sandhu et al. (2015)","archived":false,"fork":false,"pushed_at":"2022-02-22T14:38:30.000Z","size":30953,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-11-01T06:04:36.606Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bblodfon.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":"2022-02-22T14:06:47.000Z","updated_at":"2022-02-22T14:07:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"be503ad5-3e13-4a5f-81b3-708ea2552bfa","html_url":"https://github.com/bblodfon/sandhu-2015","commit_stats":{"total_commits":7,"total_committers":1,"mean_commits":7.0,"dds":0.0,"last_synced_commit":"79e7c98ecac988a198af83dd5347f311265c2a5e"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bblodfon/sandhu-2015","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Fsandhu-2015","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Fsandhu-2015/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Fsandhu-2015/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Fsandhu-2015/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bblodfon","download_url":"https://codeload.github.com/bblodfon/sandhu-2015/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bblodfon%2Fsandhu-2015/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35599679,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-17T02:00:06.162Z","response_time":116,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-10-01T14:43:02.659Z","updated_at":"2026-07-18T00:12:18.467Z","avatar_url":"https://github.com/bblodfon.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# sandu-2015\n\nAn attempt to reproduce the mRNA and miRNA expression matrices and raw data preprocessing pipelines from the following publication: \n\nSandhu, V., Bowitz Lothe, I. M., Labori, K. J., Lingjærde, O. C., Buanes, T., Dalsgaard, A. M., … Kure, E. H. (2015). Molecular signatures of mRNAs and miRNAs as prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas. Molecular Oncology, 9(4), 758–771. https://doi.org/10.1016/J.MOLONC.2014.12.002\n\nThe raw data are publicly available here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60980 (GSE60980_RAW.tar)\n\n# Reproducibility Notes\n\nIn general we couldn't get exactly the same matrices, but we did get some using diffent methods from the [AgiMicroRna](https://bioconductor.org/packages/release/bioc/html/AgiMicroRna.html) `R` package (v2.36).\n\nSome notes:\n\n- `reproduce.R`: use MRA normalization on both mRNA and miRNA data seems to be the best option in terms of number of produced features\n- `select_var_features.R`: remove features that are not variable enough (as was done in the paper)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbblodfon%2Fsandhu-2015","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbblodfon%2Fsandhu-2015","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbblodfon%2Fsandhu-2015/lists"}