{"id":19630538,"url":"https://github.com/mahshaaban/intro_data_r","last_synced_at":"2025-04-28T06:31:56.227Z","repository":{"id":44432491,"uuid":"482114805","full_name":"MahShaaban/intro_data_r","owner":"MahShaaban","description":"A gentle introduction to data analysis in R","archived":false,"fork":false,"pushed_at":"2023-08-08T13:16:23.000Z","size":4728,"stargazers_count":5,"open_issues_count":0,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-08-08T14:57:16.971Z","etag":null,"topics":["data-analysis","image-analysis","qpcr-analysis","r"],"latest_commit_sha":null,"homepage":"https://www.mahshaaban.com/courses/1116","language":"Dockerfile","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/MahShaaban.png","metadata":{"files":{"readme":"README.md","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}},"created_at":"2022-04-16T00:07:19.000Z","updated_at":"2022-07-25T04:55:30.000Z","dependencies_parsed_at":"2022-09-13T15:27:42.977Z","dependency_job_id":null,"html_url":"https://github.com/MahShaaban/intro_data_r","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MahShaaban%2Fintro_data_r","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MahShaaban%2Fintro_data_r/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MahShaaban%2Fintro_data_r/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MahShaaban%2Fintro_data_r/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MahShaaban","download_url":"https://codeload.github.com/MahShaaban/intro_data_r/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":["data-analysis","image-analysis","qpcr-analysis","r"],"created_at":"2024-11-11T12:02:55.851Z","updated_at":"2024-11-11T12:02:56.711Z","avatar_url":"https://github.com/MahShaaban.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build and push Docker image](https://github.com/MahShaaban/intro_data_r/actions/workflows/docker-image.yml/badge.svg)](https://github.com/MahShaaban/intro_data_r/actions/workflows/docker-image.yml)\n[![Deploy tutorials](https://github.com/MahShaaban/intro_data_r/actions/workflows/deploy-tutorials.yml/badge.svg)](https://github.com/MahShaaban/intro_data_r/actions/workflows/deploy-tutorials.yml)\n\n## Introduction to data analysis in R\n\n### Description\n\nThis is a short course on data analysis in R. The goal is to get the \nparticipants familiar with R code and to appreciate it as a tool to handle\ncommon experimental data. The materials are delivered in the form of \nlectures and interactive exercises.\n\n### Objectives\n\n- To get familiar with R as a tool for data analysis\n- To apply basic arithmetic and statistics in R\n- To learn to handle experimental data in R (qPCR and images)\n\n### Format\n\nEach module is delivered in three steps\n\n- [`lectures/`](lectures/): slides discussing the main concepts\n- [`practice/`](practice/): interactive exercises for practicing purposes\n- [`homework/`](homework/): more exercises to test understanding\n\n### Outline\n\n- Getting started in R\n    - Lecture ([Slides](lectures/lecture_1.pdf))\n    - Practice ([Link](https://bcmslab.shinyapps.io/practice_1/))\n    - Homework ([Link](https://bcmslab.shinyapps.io/homework_1/))\n- Basic statistics in R\n    - Lecture ([Slides](lectures/lecture_2.pdf))\n    - Practice ([Link](https://bcmslab.shinyapps.io/practice_2/))\n    - Homework ([Link](https://bcmslab.shinyapps.io/homework_2/))\n- Quantifying mRNA using the `pcr` package\n    - Lecture ([Slides](lectures/lecture_3.pdf))\n    - Practice ([Link](https://bcmslab.shinyapps.io/practice_3/))\n    - Homework ([Link](https://bcmslab.shinyapps.io/homework_3/))\n- Quantifying protein co-localization in fluorescence images using the `colocr` package\n    - Lecture ([Slides](lectures/lecture_4.pdf))\n    - Practice ([Link](https://bcmslab.shinyapps.io/practice_4/))\n    - Homework ([Link](https://bcmslab.shinyapps.io/homework_4/))\n\n### Readings\n\n- Tidy data by Hadley Wickham ([Link](https://www.jstatsoft.org/article/view/v059i10))\n- Ahmed M, Kim DR. pcr: an R package for quality assessment, analysis and \ntesting of qPCR data. PeerJ. 2018 Mar 16;6:e4473. \ndoi: [10.7717/peerj.4473](https://pubmed.ncbi.nlm.nih.gov/29576953/).\n- Ahmed M, Lai TH, Kim DR. colocr: an R package for conducting co-localization\nanalysis on fluorescence microscopy images. PeerJ. 2019;7:e7255.\ndoi:[10.7717/peerj.7255](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612416/)\n\n### Resources (what to learn next?)\n\n- Introduction to R ([Data Camp Free Interactive Course](https://www.datacamp.com/courses/free-introduction-to-r))\n- Intermediate R Course ([Data Camp Free Interactive Course](https://www.datacamp.com/courses/intermediate-r))\n- R for Data Science ([Book](https://www.amazon.co.jp/-/en/Hadley-Wickham/dp/1491910399))\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmahshaaban%2Fintro_data_r","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmahshaaban%2Fintro_data_r","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmahshaaban%2Fintro_data_r/lists"}