{"id":22308631,"url":"https://github.com/sysbiochalmers/reproduce","last_synced_at":"2026-03-19T22:22:51.268Z","repository":{"id":39406585,"uuid":"140708206","full_name":"SysBioChalmers/reproduce","owner":"SysBioChalmers","description":"Assesing the quality and reproducibility of absolute proteomic data","archived":false,"fork":false,"pushed_at":"2021-02-26T17:41:34.000Z","size":45977,"stargazers_count":1,"open_issues_count":2,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-30T22:51:20.661Z","etag":null,"topics":["proteomics","reproducible-research"],"latest_commit_sha":null,"homepage":null,"language":"PostScript","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/SysBioChalmers.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-07-12T12:08:38.000Z","updated_at":"2023-08-13T21:23:42.000Z","dependencies_parsed_at":"2022-09-08T09:42:46.046Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/reproduce","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Freproduce","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Freproduce/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Freproduce/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Freproduce/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/reproduce/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245571139,"owners_count":20637285,"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":["proteomics","reproducible-research"],"created_at":"2024-12-03T20:14:46.977Z","updated_at":"2026-01-05T09:46:15.865Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"PostScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"reproduce\n=========\n\n[![DOI](https://zenodo.org/badge/140708206.svg)](https://zenodo.org/badge/latestdoi/140708206)\n\nAssessing the quality and reproducibility of absolute proteomic data. Companion repository to the publication [_\"Benchmarking accuracy and precision of intensity‐based absolute quantification of protein abundances in Saccharomyces cerevisiae\"_](https://doi.org/10.1002/pmic.202000093).\n\nThis repository is administered by Benjamín J. Sánchez ([@BenjaSanchez](https://github.com/benjasanchez)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.\n\nRequirements\n------------\n\n* [R](https://www.r-project.org/) (tested with v3.6)\n* [RStudio](https://rstudio.com/) (tested with v1.2)\n* [Rtools](https://cran.r-project.org/bin/windows/Rtools/) (in case of a windows setup)\n* [Git](https://git-scm.com/) (or any Git client of your choice, e.g. [Github Desktop](https://desktop.github.com/))\n\nInstallation\n------------\n\n* Clone locally this repository.\n* From the command window in RStudio, run each line in `requirements.txt`.\n\nUsage\n-----\n\nAll analysis can be reproduced by knitting the RMarkdown file `code/iBAQstudy.Rmd`\n\nRepository Structure\n--------------------\n\n    |- code/            # all programmatic code relating to the project\n    |  +- templates/    # scripts for generating template files\n    |\n    |- data/            # all data from the study\n    |  |- raw_internal/ # raw data generated in-lab or by collaborators, will not be altered\n    |  |- raw_external/ # data from third-party sources, databases etc, will not be altered\n    |     +- colormaps/ # color palettes used for all figures\n    |\n    |- doc/             # documentation for the study and other explanatory material\n    |  +- paper/        # contains the generated pdf from knitting the markdown file\n    |\n    |- results          # all output from workflows and analyses\n    |  |- figures/      # graphs, designated for manuscript figures\n    |  +- pictures/     # diagrams, images, and other non-graph graphics\n    |\n    |- .gitignore       # files that will not sync to Github\n    |- LICENSE          # license\n    |- README.md        # the top level description of content\n    |- reproduce.Rproj  # contains project information used to customize the behavior of RStudio  \n    +- requirements.txt # the requirements file for reproducing the analysis environment\n\nAcknowledgements\n----------------\n\nThe initial file and directory structure of this project was developed by a group of participants in the Reproducible Science Curriculum Workshop, held at [NESCent] in December 2014. The structure is based on, and heavily follows the one proposed by [Noble 2009], with a few but small modifications. The [original repository] has been modified to the [reproducible-research-init repository] and adapted to this project.\n\n[original repository]: https://github.com/Reproducible-Science-Curriculum/rr-init\n[reproducible-research-init repository]: https://github.com/EngqvistLab/reproducible-research-init\n[NESCent]: http://nescent.org\n[Noble 2009]: http://dx.doi.org/10.1371/journal.pcbi.1000424\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Freproduce","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Freproduce","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Freproduce/lists"}