{"id":25176081,"url":"https://github.com/quantgen/lab-fall-2015","last_synced_at":"2026-01-31T14:32:46.933Z","repository":{"id":92124960,"uuid":"41869137","full_name":"QuantGen/LAB-FALL-2015","owner":"QuantGen","description":null,"archived":false,"fork":false,"pushed_at":"2015-12-09T18:24:10.000Z","size":19286,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":19,"default_branch":"master","last_synced_at":"2025-06-12T02:06:54.149Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":false,"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/QuantGen.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}},"created_at":"2015-09-03T15:57:09.000Z","updated_at":"2020-01-14T17:14:16.000Z","dependencies_parsed_at":"2023-05-15T13:30:52.455Z","dependency_job_id":null,"html_url":"https://github.com/QuantGen/LAB-FALL-2015","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/QuantGen/LAB-FALL-2015","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2015","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2015/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2015/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2015/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/QuantGen","download_url":"https://codeload.github.com/QuantGen/LAB-FALL-2015/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2015/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28945662,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-31T14:26:55.697Z","status":"ssl_error","status_checked_at":"2026-01-31T14:26:52.545Z","response_time":128,"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":"2025-02-09T13:16:01.813Z","updated_at":"2026-01-31T14:32:46.913Z","avatar_url":"https://github.com/QuantGen.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Lab Meetings QuantGen Group Fall 2015\n\n[Group's Website](http://quantgen.github.io/)\n\n### Contact:\n   - *Mengying Sun* (msun@epi.msu.edu)\n   \n   - *Gustavo de los Campos* (gustavoc@msu.edu)\n\nThis season we will be covering 8-10 papers plus 2-3 sections on software.\n\nPapers should either: (a) introduce novel metholdology that is relevant to the topics of research of interest of the group, or (b) be relevant to the particular applications you are working on. \n\nSoftware: we will organize 2-3 sections where we will share what are we developing in terms of software. \n\n\n### Schedule\n\n--------------------------------------\n\n * **Date**:  Thursday, Sept. 10, 015\n * **Time**: 1:30-2:30\n * **Place**: East Conference Room.\n * **Presenter(s)**: Alexander Grueneberg  \u0026 Gustavo de los Campos\n * **Topic(s)**:     Introductions/BGData and related software/Parallel computing in R.    \n * **Materials**:    \n    - [BGData](https://github.com/QuantGen/BGData) \n    - [BEDMatrix](https://github.com/QuantGen/BEDMatrix)\n    - [SymDMatrix](https://github.com/gdlc/symDMatrix) \n  \n-----------------------------------\n\n * **Date**: Thursday, Sept. 17, 2015\n * **Time**: 12:00-1:00\n * **Place**: East Conference Room.\n * **Presenter(s)**: Alexander Grueneberg  \n * **Topic(s)**: Parallel computing in R using the parallel package\n * **Materials**:    \n    - [Slides](https://docs.google.com/presentation/d/1fLX0d65FZAEOJ1MA-TZtvRSnnks45BfbsRzfWNuIXkI/edit?usp=sharing)\n    - [Code](https://gist.github.com/agrueneberg/2a9649bcf858193b69db)\n    - [parallel Package Vignette](https://stat.ethz.ch/R-manual/R-devel/library/parallel/doc/parallel.pdf)\n\n-----------------------------------\n\n * **Date**:  Thursday, Sept. 24, 2015\n * **Time**: 12:00-1:00\n * **Place**: East Conference Room.\n * **Presenter(s)**: Marco Lopez-Cruz\n * **Topic(s)**:     Factor Analysis, High-dimensional mixed models\n * **Materials**:    \n    * [Article](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Marco_Paper_Factor%20Analysis.pdf)\n    * [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Marco_Slides_Factor%20Analysis.pdf)\n \n-----------------------------------\n\n  * **Date**:  Thursday, Oct. 15, 2015\n  * **Time**:  12:00-1:00\n  * **Place**: East Conference Room\n  * **Presenter(s)**: Felix Enciso \n  * **Topic(s)**: GWAS with tetraploids: background theory, ideas and pilot aplication.  \n  * **Materials:**\n    * [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Felix_Slides_Genomic%20Approximation.pdf)\n    \n--------------------------------------\n\n  * **Date**:  Thursday, Oct. 22, 2015\n  * **Time**: 12:00-1:00\n  * **Place**: East Conference Room\n  * **Presenter(s)**: Yeni\n  * **Topic(s)**: Fast GWAS using Ridge-regression type methods.     \n  * **Materials:**\n    * [Article](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Yeni_Paper_Gualdron%20Duarte%20et%20al%202014.pdf)\n    * [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Yeni_Slides_Rapid%20Screening.pdf)\n    \n--------------------------------------\n\n  * **Date**:  Thursday, Nov. 5, 2015\n  * **Time**: 12:00-1:00\n  * **Place**: East Conference Room\n  * **Presenter(s)**: Mengying\n  * **Topic(s)**: Research related to Gout     \n  * **Materials:**\n    * [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Mengying_Slides_Gout.pdf)\n    * [Appendix](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Mengying_Appendix_Gout.xlsx)\n\n    \n--------------------------------------------\n\n  * **Date**:  Thursday, Nov. 12, 2015\n  * **Time**: 12:00-1:00\n  * **Place**: East Conference Room\n  * **Presenter(s)**: Lian Lian\n  * **Topic(s)**: SKAT and Score test for multiple random effects\n  * **Materials:**: \n    * [Article](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Lian_Paper_SKAT.pdf)\n    * [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Lian_Slides_SKAT.pdf)\n    * [Software](https://github.com/lian0090/SKAT2)\n    \n--------------------------------------------\n  * **Date**:  Thursday, Nov. 19, 2015\n  * **Time**: 12:00-1:00\n  * **Place**: East Conference Room\n  * **Presenter(s)**: Sudha Veturi\n  * **Topic(s)**:   Genetic correlation for quantitative human traits\n  * **Materials:**: \n    * [Article](http://biorxiv.org/content/early/2015/01/27/014498)\n    * [Slides](https://sudhaveturi.shinyapps.io/LabMeeting)\n    \n    \n--------------------------------------------\n\n\n### Ideas for articles\n\nIf you have a paper you would like to present, use that one, otherwise feel free to choose one from this list\n\n* [Fan et al. (Functional Linear (Meta) Analyses)](http://www.genetics.org/content/200/4/1089.full.pdf+html)\n* [Bryc et al. (Ancestry in the US)](The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States)\n* [ Sullivan et al. (Atlas of Genetic Correlation)](http://biorxiv.org/content/early/2015/01/27/014498) . You may want to discuss this paper in the light of this one: [link](http://www.genetics.org/content/early/2015/07/23/genetics.115.179978.abstract).\n* [Gerstberger, et al., Protein-binding RNA](http://www.nature.com/nrg/journal/v15/n12/full/nrg3813.html).\n* [Lu et al. high-throughput analysis of gene effects ] (http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg4008.html)\n* [ Jiang et al. (Misspecified Mixed Models)](http://arxiv.org/abs/1404.2355 )  [did we discuss it last Fall?]\n* [ Yang et al. (Mixed model assoc. analyses)](http://www.nature.com/ng/journal/v46/n2/full/ng.2876.html).\n* Random Regressions: [Meyer (1997)](http://www.biomedcentral.com/content/pdf/1297-9686-30-3-221.pdf), [Kirkpatrick \u0026 Meyer (2004)](http://www.genetics.org/content/168/4/2295.short).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantgen%2Flab-fall-2015","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantgen%2Flab-fall-2015","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantgen%2Flab-fall-2015/lists"}