{"id":18501644,"url":"https://github.com/const-ae/transformgampoi-paper","last_synced_at":"2026-02-15T14:31:09.345Z","repository":{"id":46733615,"uuid":"378103949","full_name":"const-ae/transformGamPoi-Paper","owner":"const-ae","description":null,"archived":false,"fork":false,"pushed_at":"2023-09-04T08:35:04.000Z","size":174983,"stargazers_count":29,"open_issues_count":4,"forks_count":7,"subscribers_count":2,"default_branch":"master","last_synced_at":"2026-01-31T16:59:26.641Z","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":"gpl-3.0","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":"LICENSE.md","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":"2021-06-18T09:44:52.000Z","updated_at":"2026-01-22T14:29:17.000Z","dependencies_parsed_at":"2024-11-06T14:04:38.916Z","dependency_job_id":null,"html_url":"https://github.com/const-ae/transformGamPoi-Paper","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/const-ae/transformGamPoi-Paper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FtransformGamPoi-Paper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FtransformGamPoi-Paper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FtransformGamPoi-Paper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FtransformGamPoi-Paper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/const-ae","download_url":"https://codeload.github.com/const-ae/transformGamPoi-Paper/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FtransformGamPoi-Paper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29481360,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-15T11:35:25.641Z","status":"ssl_error","status_checked_at":"2026-02-15T11:34:57.128Z","response_time":118,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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":"2024-11-06T13:54:28.367Z","updated_at":"2026-02-15T14:31:09.330Z","avatar_url":"https://github.com/const-ae.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Online Supplement of _Comparison of Transformations for Single-Cell RNA-Seq Data_ \n\n[![DOI](https://zenodo.org/badge/378103949.svg)](https://zenodo.org/badge/latestdoi/378103949)\n\n\nThis repository contains the code to generate the figures of our paper 'Comparison of Transformations for Single-Cell RNA-Seq Data' in Nature Methods https://www.nature.com/articles/s41592-023-01814-1. \n\nThe accompanying R package `transformGamPoi` is available via [Bioconductor](https://bioconductor.org/packages/transformGamPoi/) or at https://github.com/const-ae/transformGamPoi. \n\nAt https://shiny-portal.embl.de/shinyapps/app/08_single-cell_transformation_benchmark, we provide an interactive website to explore the benchmark results. The underlying source code is available at https://github.com/const-ae/transformGamPoi-ShinyApp.\n\n\n# Repository content\n\nThe repository is organized into four folders. The root directory contains some additional files for documentation and data plumbing purposes.\n\n* **benchmark** contains the infrastructure for our benchmark of 22 different transformation methods. The [job_overview.yaml](https://github.com/const-ae/transformGamPoi-Paper/blob/master/benchmark/job_overview.yaml) is a declarative specification of all the parameter combinations (more than 58,000) that we benchmarked. The [renv.lock](https://github.com/const-ae/transformGamPoi-Paper/blob/master/benchmark/renv.lock) file contains detailed information about each R package that was used in the benchmark using the [`renv`](https://rstudio.github.io/renv/articles/renv.html) system.\n* **notebooks** contains the Rmd scripts to generate the plots shown in the manuscript. Links to the rendered HTML notebooks are below\n* **illustrations** and **output** contain the figures\n\n# Code to generate figures\n\n* [Figure 1](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_concept_overview_figure.html): Conceptual differences between variance-stabilizing transformations\n* [Figure 2](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_benchmark_results.html): Benchmark results\n* [Figure 3](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_benchmark_results.html): Computational expense\n* [Figure 4](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_benchmark_contrasts.html): Comparison of selected transformations\n--------\n* [plot_size_factor_effect_on_dim_reduction.Rmd](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_size_factor_effect_on_dim_reduction.html) generates Extended Data Fig. S1.\n* [plot_variance_stabilization_results.Rmd](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_variance_stabilization_results.html) generates Extended Data Fig. S2.\n* [plot_bimodal_gene_histograms.Rmd](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_bimodal_gene_histograms.html) generates Extended Data Fig. S3.\n* [plot_dataset_structure.Rmd](https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_dataset_structure.html) generates Suppl. Figs. S1, Extended Data Fig. S5, and Suppl. Tabl. S1.\n* [plot_benchmark_results.Rmd](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_benchmark_results.html) generates Extended Data Figs. S6, S7, in addition to Fig. 2 and 3.\n* [plot_deep_sequenced_overlap.Rmd](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_deep_sequenced_overlap.html) generates Extended Data Fig. S8.\n* [plot_clustering_results.Rmd](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_clustering_results.html) generates Extended Data Fig. S9.\n* [plot_stratified_performance.Rmd](https://htmlpreview.github.io/?https://github.com/const-ae/transformGamPoi-Paper/blob/master/notebooks/plot_stratified_performance.html) generates Extended Data Figs. S10.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Ftransformgampoi-paper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fconst-ae%2Ftransformgampoi-paper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Ftransformgampoi-paper/lists"}