{"id":26448829,"url":"https://github.com/adeschen/signatureheatmap","last_synced_at":"2025-03-18T14:42:32.408Z","repository":{"id":62858875,"uuid":"561865445","full_name":"adeschen/SignatureHeatmap","owner":"adeschen","description":"R package to create heatmaps using signature gene list and transcriptomic data","archived":false,"fork":false,"pushed_at":"2023-03-14T02:40:06.000Z","size":2029,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2023-09-02T20:43:10.753Z","etag":null,"topics":["classification","gene-list","gene-signature","heatmap","heatmap-visualization","r","rna-seq-data"],"latest_commit_sha":null,"homepage":"https://adeschen.github.io/SignatureHeatmap/","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/adeschen.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":"2022-11-04T17:05:05.000Z","updated_at":"2023-09-02T20:43:35.216Z","dependencies_parsed_at":"2023-09-02T20:59:05.790Z","dependency_job_id":null,"html_url":"https://github.com/adeschen/SignatureHeatmap","commit_stats":null,"previous_names":["adeschen/signatureheatmap"],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adeschen%2FSignatureHeatmap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adeschen%2FSignatureHeatmap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adeschen%2FSignatureHeatmap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adeschen%2FSignatureHeatmap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/adeschen","download_url":"https://codeload.github.com/adeschen/SignatureHeatmap/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244243679,"owners_count":20422113,"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":["classification","gene-list","gene-signature","heatmap","heatmap-visualization","r","rna-seq-data"],"created_at":"2025-03-18T14:42:31.911Z","updated_at":"2025-03-18T14:42:32.398Z","avatar_url":"https://github.com/adeschen.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- badges: start --\u003e\n[![R-CMD-check-bioc](https://github.com/adeschen/SignatureHeatmap/actions/workflows/check-bioc.yaml/badge.svg)](https://github.com/adeschen/SignatureHeatmap/actions/workflows/check-bioc.yaml)\n[![codecov](https://codecov.io/gh/adeschen/SignatureHeatmap/branch/main/graph/badge.svg?token=XVKU8S1E2R)](https://codecov.io/gh/adeschen/SignatureHeatmap)\n[![License: Artistic-2.0](https://img.shields.io/badge/License-Artistic%202.0-0298c3.svg)](https://opensource.org/licenses/Artistic-2.0)\n\u003c!-- badges: end --\u003e\n\n# SignatureHeatmap\n\nThe __SignatureHeatmap__ package enables signature classification of tumor \nsamples by generating heatmaps using transcriptomic data. \n\nAt the moment, three different lists of signature genes are \navailable in the __SignatureHeatmap__ package: \n\n* the original list of basal/classical genes from Moffitt et al. 2015 for \npancreatic ductal adenocarcinoma (PDAC) tissue samples\n* the updated list of basal/classical genes for PDAC tissue samples \nfrom Miyabayashi et al. 2020\n* the list of basal/classical genes from Tiriac et al. 2018 that has been \ndeveloped for PDAC organoids\n\n\n## Authors ##\n\n[Astrid Desch\u0026ecirc;nes](http://ca.linkedin.com/in/astriddeschenes \"Astrid Desch\u0026ecirc;nes\"),\nDaniel King and\nDavid A. Tuveson\n\n\n## Citation ##\n\nIf you use this package for a publication, we would ask you \nto cite the following:\n\n\u003e Deschênes A, King D and Tuveson DA. SignatureHeatmap: Heatmap using signature gene list and RNA-seq expression data. R package version 0.0.3, https://adeschen.github.io/SignatureHeatmap/ \n  \nYou can also replace the latest by the Research Resource Identifier __(RRID)__, as \nexample:\n\n\u003e   SignatureHeatmap version 0.0.4, RRID: SCR_022949\n\nIf you use one of the available signature gene list, the appropriate\npaper should be referenced.\n\nFor Moffitt et al. 2015\n\n\u003e Moffitt RA, Marayati R, Flate EL et al. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nat Genet. 2015 Oct;47(10):1168-78. doi: 10.1038/ng.3398. Epub 2015 Sep 7. PMID: 26343385; PMCID: PMC4912058.\n\nFor Tiriac et al. 2018\n\n\u003e Tiriac H, Belleau P, Engle DD et al. Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer. Cancer Discov. 2018 Sep;8(9):1112-1129. doi: 10.1158/2159-8290.CD-18-0349. Epub 2018 May 31. PMID: 29853643; PMCID: PMC6125219.\n\nFor Miyabayashi et al. 2020\n\n\u003e Miyabayashi K, Baker LA, Deschênes A et al. Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes. Cancer Discov. 2020 Oct;10(10):1566-1589. doi: 10.1158/2159-8290.CD-20-0133. Epub 2020 Jul 23. PMID: 32703770; PMCID: PMC7664990.\n\n\n## Documentation ##\n\n[SignatureHeatmap Website](https://adeschen.github.io/SignatureHeatmap/)\n\n[SignatureHeatmap Get Started](https://adeschen.github.io/SignatureHeatmap/articles/SignatureHeatmap.html)\n\n## Installation ##\n\nTo install the latest version accessible using the [devtools](https://cran.r-project.org/web/packages/devtools/index.html) \npackage:\n\n     ## Load required package\n     library(devtools)\n\n     ## Install the latest version of SignatureHeatmap\n     devtools::install_github('adeschen/SignatureHeatmap')\n\n\n\n## Maintainer\n\n[Astrid Desch\u0026ecirc;nes](https://github.com/adeschen/ \"Astrid Desch\u0026ecirc;nes\")\n\n\n## Bugs/Feature requests ##\n\n[Please contact us](https://github.com/adeschen/SignatureHeatmap/issues) for bug fixes or with feature requests. \n\nThanks!\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadeschen%2Fsignatureheatmap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fadeschen%2Fsignatureheatmap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadeschen%2Fsignatureheatmap/lists"}