{"id":21023868,"url":"https://github.com/biogenies/countfitter-simulations","last_synced_at":"2026-02-11T15:01:45.196Z","repository":{"id":73085132,"uuid":"277082259","full_name":"BioGenies/countfitteR-simulations","owner":"BioGenies","description":null,"archived":false,"fork":false,"pushed_at":"2020-09-09T15:16:08.000Z","size":4122,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-10-10T13:37:08.701Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"PostScript","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/BioGenies.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,"zenodo":null}},"created_at":"2020-07-04T09:49:59.000Z","updated_at":"2020-09-30T11:39:23.000Z","dependencies_parsed_at":null,"dependency_job_id":"d5e54397-4574-4cb9-8a3e-b4966a2f5cc6","html_url":"https://github.com/BioGenies/countfitteR-simulations","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BioGenies/countfitteR-simulations","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2FcountfitteR-simulations","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2FcountfitteR-simulations/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2FcountfitteR-simulations/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2FcountfitteR-simulations/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioGenies","download_url":"https://codeload.github.com/BioGenies/countfitteR-simulations/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2FcountfitteR-simulations/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29336013,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-11T14:34:07.188Z","status":"ssl_error","status_checked_at":"2026-02-11T14:34:06.809Z","response_time":97,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2024-11-19T11:20:34.727Z","updated_at":"2026-02-11T15:01:45.173Z","avatar_url":"https://github.com/BioGenies.png","language":"PostScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Read me\n\nThis repository contains data and code necessary to reproduce analysis from the article: Jarosław Chilimoniuk, Alicja Gosiewska, Jadwiga Słowik, Romano Weiss, Stefan Rödiger, and Michał Burdukiewicz. countfitteR: count data analysis for precision medicine.\n\nThe analysis conducted in this article resulted in a framework for the automatic selection of the appropriate count distribution CountfitteR, available as an *R* package (https://CRAN.R-project.org/package=countfitteR) and a web server (TO DO).\n\n## How to reproduce the main part of the analysis?\n\nRun `scripts/countfitter_simulations.R` and `scripts/two_step_simulations.R`. The first script performs simulations for countfitteR, the second script performs simulations for Two-Step-Procedure.\n\n## How to generate results and plots for publication?\n\nRun `scripts/plots.R` to generate plots included in the article and supplementary articles.\n\nRun `scripts/supplementary_tables.R` to generate tables included in the supplementary materials.\n\nRun `scripts/mean_power_table.R` to generate Table 2.\n\n## Repository strcture\n\nAll scripts are in the folder `scripts`.\nPartial results saved as binary R data files are in the folder `data`.\nData and plots are in the folder `files`.\n\n## R Session information\n\nAll scripts used in this study are compatible with following version of R:\n\n**R version 3.6.1 (2019-07-05)**\n\n**Platform:** x86_64-w64-mingw32/x64 (64-bit) \n\n**locale:**\n_LC_COLLATE=Polish_Poland.1250_, _LC_CTYPE=Polish_Poland.1250_, _LC_MONETARY=Polish_Poland.1250_, _LC_NUMERIC=C_ and _LC_TIME=Polish_Poland.1250_\n\n**attached base packages:** \n_stats_, _graphics_, _grDevices_, _datasets_, _utils_, _methods_ and _base_\n\n**other attached packages:** \n_MASS(v.7.3-51.6)_, _pscl(v.1.5.5)_, _pbapply(v.1.4-2)_, _countfitteR(v.1.2)_, _gt(v.0.2.1)_, _xtable(v.1.8-4)_, _patchwork(v.1.0.1)_, _latex2exp(v.0.4.0)_, _tidyr(v.1.0.2)_, _dplyr(v.0.8.5)_, _ggh4x(v.0.1.0.9000)_, _ggplot2(v.3.3.2)_ and _readr(v.1.3.1)_\n\n**loaded via a namespace (and not attached):** \n_Rcpp(v.1.0.4.6)_, _later(v.1.0.0)_, _pillar(v.1.4.4)_, _compiler(v.3.6.1)_, _tools(v.3.6.1)_, _digest(v.0.6.25)_, _lifecycle(v.0.2.0)_, _tibble(v.3.0.1)_, _gtable(v.0.3.0)_, _pkgconfig(v.2.0.3)_, _rlang(v.0.4.6)_, _shiny(v.1.4.0.2)_, _rstudioapi(v.0.11)_, _parallel(v.3.6.1)_, _fastmap(v.1.0.1)_, _withr(v.2.2.0)_, _stringr(v.1.4.0)_, _vctrs(v.0.3.1)_, _hms(v.0.5.3)_, _grid(v.3.6.1)_, _tidyselect(v.1.0.0)_, _glue(v.1.4.1)_, _R6(v.2.4.1)_, _pander(v.0.6.3)_, _purrr(v.0.3.3)_, _magrittr(v.1.5)_, _promises(v.1.1.0)_, _htmltools(v.0.4.0)_, _scales(v.1.1.1)_, _ellipsis(v.0.3.1)_, _assertthat(v.0.2.1)_, _mime(v.0.9)_, _colorspace(v.1.4-1)_, _httpuv(v.1.5.2)_, _renv(v.0.11.0)_, _stringi(v.1.4.6)_, _munsell(v.0.5.0)_ and _crayon(v.1.3.4)_\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Fcountfitter-simulations","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiogenies%2Fcountfitter-simulations","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Fcountfitter-simulations/lists"}