{"id":14067715,"url":"https://github.com/sebastiz/EndoMineR","last_synced_at":"2025-07-30T02:31:19.761Z","repository":{"id":133729126,"uuid":"180203938","full_name":"sebastiz/EndoMineR","owner":"sebastiz","description":"Endoscopic and Pathological data extraction for various endo-pathological data extraction","archived":false,"fork":true,"pushed_at":"2023-03-07T16:55:13.000Z","size":55433,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"dev2","last_synced_at":"2024-12-04T08:36:30.668Z","etag":null,"topics":["cancer-research","endoscopy","gastroenterology","peer-reviewed","r","r-package","rstats","semi-structured-data","text-mining"],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"ropensci/EndoMineR","license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sebastiz.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":".github/FUNDING.yml","license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null},"funding":{"github":null,"patreon":null,"open_collective":null,"ko_fi":null,"tidelift":null,"community_bridge":null,"liberapay":null,"issuehunt":null,"otechie":null,"custom":"https://www.health.org.uk/funding-and-partnerships/programmes/improving-lesion-recognition-using-routinely-collected-endos"}},"created_at":"2019-04-08T17:55:30.000Z","updated_at":"2021-10-04T12:38:23.000Z","dependencies_parsed_at":"2023-09-21T20:02:15.295Z","dependency_job_id":null,"html_url":"https://github.com/sebastiz/EndoMineR","commit_stats":{"total_commits":542,"total_committers":6,"mean_commits":90.33333333333333,"dds":0.01845018450184499,"last_synced_commit":"a2c676864a39486c8f684fb502b0a9d3c760ff93"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/sebastiz/EndoMineR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastiz%2FEndoMineR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastiz%2FEndoMineR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastiz%2FEndoMineR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastiz%2FEndoMineR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sebastiz","download_url":"https://codeload.github.com/sebastiz/EndoMineR/tar.gz/refs/heads/dev2","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastiz%2FEndoMineR/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267798625,"owners_count":24145727,"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","status":"online","status_checked_at":"2025-07-30T02:00:09.044Z","response_time":70,"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":["cancer-research","endoscopy","gastroenterology","peer-reviewed","r","r-package","rstats","semi-structured-data","text-mining"],"created_at":"2024-08-13T07:05:44.492Z","updated_at":"2025-07-30T02:31:18.124Z","avatar_url":"https://github.com/sebastiz.png","language":"R","funding_links":["https://www.health.org.uk/funding-and-partnerships/programmes/improving-lesion-recognition-using-routinely-collected-endos"],"categories":["R"],"sub_categories":[],"readme":"\n\n---\noutput: github_document\n---\n\n\n[![Build Status](https://travis-ci.org/sebastiz/EndoMineR.svg?branch=master)](https://travis-ci.org/sebastiz/EndoMineR)\n[![ropensci](https://badges.ropensci.org/153_status.svg)](https://github.com/ropensci/onboarding/issues/153)\n[![Coverage status](https://codecov.io/gh/sebastiz/EndoMineR/branch/master/graph/badge.svg)](https://codecov.io/github/sebastiz/EndoMineR?branch=master)\n\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nlibrary(pander)\nlibrary(EndoMineR)\nlibrary(here)\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"README-\"\n)\n```\n\n\nThis package has undergone a major revision to make it much more user friendly. THe documentation has been updated to reflect this. I am always happy to hear of any feedback, positive and negative.\n\n## **Aims of EndoMineR**\n\nThe goal of EndoMineR is to extract as much information as possible from free or semi-structured endoscopy reports and their associated pathology specimens.  A full tutorial can be found [here](https://docs.ropensci.org/EndoMineR/articles/EndoMineR.html)\n\n## Installation\n\nYou can install EndoMineR from github with:\n\n```{r gh-installation, eval = FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"ropenSci/EndoMineR\")\n```\n\nIf you dont have access to github, then download the zip and change the working dirctory to the place you have downloaded it, then do\n\n```{r gh-installation2, eval = FALSE}\nsetwd(\"C:/Users/Desktop/\")\n\n#On windows you cand cd to change the directory or us pushd to create a temporary directory indtead of cd and then setwd to the temporary directory\nunzip(\"EndoMineR.zip\")\nfile.rename(\"EndoMineR.zip-master\", \"EndoMineR.zip\")\nshell(\"R CMD build EndoMineR.zip\")\n\n#Then install the resulting tarball with:\n\ninstall.packages(\"EndoMineR_0.2.0.9000.tar.gz\", repos = NULL)\n```\n\n\n### How to contribute\n\nContributions to this project are most welcome. There are just a few small guidelines you need to follow.\n\n#### Submitting a patch\n\nIt's generally best to start by opening a new issue describing the bug or feature you're intending to fix. Even if you think it's relatively minor, it's helpful to know what people are working on. Mention in the initial issue that you are planning to work on that bug or feature so that it can be assigned to you.\n\nFollow the normal process of forking the project, and setup a new branch to work in. It's important that each group of changes be done in separate branches in order to ensure that a pull request only includes the commits related to that bug or feature.\n\nThe best way to ensure your code is properly formatted is to use lint. Various packages in R provide this.\n\nAny significant changes should almost always be accompanied by tests. The project already has good test coverage, so look at some of the existing tests if you're unsure how to go about it. \n\nDo your best to have well-formed commit messages for each change. This provides consistency throughout the project, and ensures that commit messages are able to be formatted properly by various git tools.\n\nFinally, push the commits to your fork and submit a pull request. Please, remember to rebase properly in order to maintain a clean, linear git history.\n\n\n[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsebastiz%2FEndoMineR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsebastiz%2FEndoMineR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsebastiz%2FEndoMineR/lists"}