{"id":16320095,"url":"https://github.com/helenalc/principled-components","last_synced_at":"2025-05-14T07:12:30.154Z","repository":{"id":181636850,"uuid":"666831366","full_name":"HelenaLC/principled-components","owner":"HelenaLC","description":null,"archived":false,"fork":false,"pushed_at":"2023-07-16T15:05:59.000Z","size":13532,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-02-17T01:29:44.727Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/HelenaLC.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}},"created_at":"2023-07-15T18:10:06.000Z","updated_at":"2023-07-15T18:10:59.000Z","dependencies_parsed_at":"2023-07-16T16:46:07.882Z","dependency_job_id":null,"html_url":"https://github.com/HelenaLC/principled-components","commit_stats":null,"previous_names":["helenalc/principled-components"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2Fprincipled-components","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2Fprincipled-components/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2Fprincipled-components/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2Fprincipled-components/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HelenaLC","download_url":"https://codeload.github.com/HelenaLC/principled-components/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254092836,"owners_count":22013294,"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":[],"created_at":"2024-10-10T22:29:04.563Z","updated_at":"2025-05-14T07:12:25.143Z","avatar_url":"https://github.com/HelenaLC.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"site is deployed at [https://helenalc.github.io/principled-components](https://helenalc.github.io/principled-components)\n\n# Food for thought\n\n- Principal Component regression (henceforth abbreviated with \"pcr\") has been\nproposed in [Büttner et al., 2019](http://doi.org/10.1038/s41592-018-0254-1)\nto assess batch correction.  \n\n- Here, pcr is performed against batches only, and scores are aggregated across\nPCs to assess the amount of variability (overall) that is attributable to batch.\n\n- [Lütge et al.](https://doi.org/10.26508/lsa.202001004) evaluates\nmetrics for batch effect quantification, and also includes pcr.\n\n- Again, pcr is performed against batch only; it comes out as being less\nsensitive (i.e., only strong effects are detected), but performs well overall.\nShould be fine, since we're not aggregating across PCs, but are interested\nin \"subtleties\" (e.g., looking at genes/clusters vs. overall variability).\n\n- Here, we aim to consider pcr against both batch and cluster, and develop an\napproach (e.g., metrics, diagnostic plots) in order to assess clustering, and\npotentially identify subpopulations that represent distinct functional states\n(that are biologically meaningful and may better be treated as distinct), or\noutliers (that should be removed).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fprincipled-components","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhelenalc%2Fprincipled-components","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fprincipled-components/lists"}