{"id":18501575,"url":"https://github.com/const-ae/glmgampoi-paper","last_synced_at":"2026-03-19T04:49:31.563Z","repository":{"id":82391846,"uuid":"287285904","full_name":"const-ae/glmGamPoi-Paper","owner":"const-ae","description":null,"archived":false,"fork":false,"pushed_at":"2020-12-28T17:26:55.000Z","size":34152,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-09-10T05:34:45.960Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","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/const-ae.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}},"created_at":"2020-08-13T13:20:57.000Z","updated_at":"2023-08-21T15:13:11.000Z","dependencies_parsed_at":"2023-04-19T23:31:57.099Z","dependency_job_id":null,"html_url":"https://github.com/const-ae/glmGamPoi-Paper","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/const-ae/glmGamPoi-Paper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FglmGamPoi-Paper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FglmGamPoi-Paper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FglmGamPoi-Paper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FglmGamPoi-Paper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/const-ae","download_url":"https://codeload.github.com/const-ae/glmGamPoi-Paper/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FglmGamPoi-Paper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28754807,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-25T13:59:49.818Z","status":"ssl_error","status_checked_at":"2026-01-25T13:59:33.728Z","response_time":113,"last_error":"SSL_read: 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":"2024-11-06T13:54:20.108Z","updated_at":"2026-01-25T15:02:33.539Z","avatar_url":"https://github.com/const-ae.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# glmGamPoi-Paper\n\n\u003e glmGamPoi: Fitting Gamma-Poisson Generalized Linear Models on Single Cell Count Data  \n\u003e Constantin Ahlmann-Eltze, Wolfgang Huber  \n\u003e Bioinformatics; 2020-12-09; doi: https://doi.org/10.1093/bioinformatics/btaa1009\n\nThis repository contains the code that was used to generate the figures for the paper that describes the [glmGamPoi](https://github.com/const-ae/glmGamPoi) package.\n\nThe scripts that call `glmGamPoi`, `DESeq2`, and `edgeR` are in the [benchmarks](https://github.com/const-ae/glmGamPoi-Paper/tree/master/benchmarks) folder:\n\n* [run_benchmark-brain20k.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_benchmark-brain20k.R)\n* [run_benchmark-mousegastrulation.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_benchmark-mousegastrulation.R)\n* [run_benchmark-pbmc4k.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_benchmark-pbmc4k.R)\n* [run_benchmark-pbmc68k.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_benchmark-pbmc68k.R)\n* [run_asymptotics_benchmark.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_asymptotics_benchmark.R)\n* [run_asymptotics_parameters_benchmark.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_asymptotics_parameters_benchmark.R)\n\nEach script was run 5 times on a cluster and the results were extracted from the log files with the `gather_XXX_results.Rmd` scripts which are in the `benchmarks` folder as well.\n\nThe [data](https://github.com/const-ae/glmGamPoi-Paper/tree/master/data) folder contains the cleaned up tables that were used to produce the plots in the paper. \n\nThe plots were generated with the [make_plots.Rmd](http://htmlpreview.github.io/?https://github.com/const-ae/glmGamPoi-Paper/blob/master/make_plots.nb.html) script.\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fglmgampoi-paper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fconst-ae%2Fglmgampoi-paper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fglmgampoi-paper/lists"}