{"id":18046656,"url":"https://github.com/ltla/pseudocount2018","last_synced_at":"2025-08-02T08:37:19.298Z","repository":{"id":82716829,"uuid":"141042430","full_name":"LTLA/PseudoCount2018","owner":"LTLA","description":"Some thoughts on choosing an appropriate pseudo-count for log-transformation of scRNA-seq counts.","archived":false,"fork":false,"pushed_at":"2018-11-19T10:39:44.000Z","size":73,"stargazers_count":9,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-06-24T07:04:56.588Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"TeX","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/LTLA.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":"2018-07-15T16:39:58.000Z","updated_at":"2023-02-28T05:44:19.000Z","dependencies_parsed_at":null,"dependency_job_id":"b73ac89d-8103-4a38-9f95-9907c080c754","html_url":"https://github.com/LTLA/PseudoCount2018","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/LTLA/PseudoCount2018","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPseudoCount2018","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPseudoCount2018/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPseudoCount2018/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPseudoCount2018/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LTLA","download_url":"https://codeload.github.com/LTLA/PseudoCount2018/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPseudoCount2018/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268355797,"owners_count":24237371,"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","status":"online","status_checked_at":"2025-08-02T02:00:12.353Z","response_time":74,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2024-10-30T19:08:24.034Z","updated_at":"2025-08-02T08:37:19.276Z","avatar_url":"https://github.com/LTLA.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Errors upon log-transformation of scRNA-seq data\n\nThis repository contains code and manuscript files for the paper **Overcoming systematic errors caused by log-transformation of normalized single-cell RNA sequencing data**\nby [Lun (2018)](https://doi.org/10.1101/404962).\n\nThe `report` subdirectory contains LaTeX files for the report.\nThe `scripts` subdirectory contains R code to reproduce the analyses described in the report:\n\n- `spurious_sim.R`, to examine the non-zero log-fold change induced by the log-transformation.\n- `substructure.R`, to examine the introduction of structural artifacts due the log-transformation.\n- `alternatives.R`, to examine the performance of other transformations.\n- `check_ercc.R`, to examine the behaviour of the log-transformation on real data.\n- `power_sim.R`, to examine the consequences on detection power with an increased pseudo-count. \n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fpseudocount2018","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fltla%2Fpseudocount2018","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fpseudocount2018/lists"}