https://github.com/quantgen/lab-fall-2015
https://github.com/quantgen/lab-fall-2015
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- Host: GitHub
- URL: https://github.com/quantgen/lab-fall-2015
- Owner: QuantGen
- Created: 2015-09-03T15:57:09.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2015-12-09T18:24:10.000Z (over 9 years ago)
- Last Synced: 2025-02-09T13:15:57.323Z (3 months ago)
- Size: 18.4 MB
- Stars: 0
- Watchers: 20
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Lab Meetings QuantGen Group Fall 2015
[Group's Website](http://quantgen.github.io/)
### Contact:
- *Mengying Sun* ([email protected])
- *Gustavo de los Campos* ([email protected])
This season we will be covering 8-10 papers plus 2-3 sections on software.
Papers 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.
Software: we will organize 2-3 sections where we will share what are we developing in terms of software.
### Schedule
--------------------------------------
* **Date**: Thursday, Sept. 10, 015
* **Time**: 1:30-2:30
* **Place**: East Conference Room.
* **Presenter(s)**: Alexander Grueneberg & Gustavo de los Campos
* **Topic(s)**: Introductions/BGData and related software/Parallel computing in R.
* **Materials**:
- [BGData](https://github.com/QuantGen/BGData)
- [BEDMatrix](https://github.com/QuantGen/BEDMatrix)
- [SymDMatrix](https://github.com/gdlc/symDMatrix)
-----------------------------------
* **Date**: Thursday, Sept. 17, 2015
* **Time**: 12:00-1:00
* **Place**: East Conference Room.
* **Presenter(s)**: Alexander Grueneberg
* **Topic(s)**: Parallel computing in R using the parallel package
* **Materials**:
- [Slides](https://docs.google.com/presentation/d/1fLX0d65FZAEOJ1MA-TZtvRSnnks45BfbsRzfWNuIXkI/edit?usp=sharing)
- [Code](https://gist.github.com/agrueneberg/2a9649bcf858193b69db)
- [parallel Package Vignette](https://stat.ethz.ch/R-manual/R-devel/library/parallel/doc/parallel.pdf)
-----------------------------------
* **Date**: Thursday, Sept. 24, 2015
* **Time**: 12:00-1:00
* **Place**: East Conference Room.
* **Presenter(s)**: Marco Lopez-Cruz
* **Topic(s)**: Factor Analysis, High-dimensional mixed models
* **Materials**:
* [Article](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Marco_Paper_Factor%20Analysis.pdf)
* [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Marco_Slides_Factor%20Analysis.pdf)
-----------------------------------
* **Date**: Thursday, Oct. 15, 2015
* **Time**: 12:00-1:00
* **Place**: East Conference Room
* **Presenter(s)**: Felix Enciso
* **Topic(s)**: GWAS with tetraploids: background theory, ideas and pilot aplication.
* **Materials:**
* [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Felix_Slides_Genomic%20Approximation.pdf)
--------------------------------------
* **Date**: Thursday, Oct. 22, 2015
* **Time**: 12:00-1:00
* **Place**: East Conference Room
* **Presenter(s)**: Yeni
* **Topic(s)**: Fast GWAS using Ridge-regression type methods.
* **Materials:**
* [Article](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Yeni_Paper_Gualdron%20Duarte%20et%20al%202014.pdf)
* [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Yeni_Slides_Rapid%20Screening.pdf)
--------------------------------------
* **Date**: Thursday, Nov. 5, 2015
* **Time**: 12:00-1:00
* **Place**: East Conference Room
* **Presenter(s)**: Mengying
* **Topic(s)**: Research related to Gout
* **Materials:**
* [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Mengying_Slides_Gout.pdf)
* [Appendix](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Mengying_Appendix_Gout.xlsx)
--------------------------------------------
* **Date**: Thursday, Nov. 12, 2015
* **Time**: 12:00-1:00
* **Place**: East Conference Room
* **Presenter(s)**: Lian Lian
* **Topic(s)**: SKAT and Score test for multiple random effects
* **Materials:**:
* [Article](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Lian_Paper_SKAT.pdf)
* [Slides](https://github.com/QuantGen/LAB-FALL-2015/blob/master/Lian_Slides_SKAT.pdf)
* [Software](https://github.com/lian0090/SKAT2)
--------------------------------------------
* **Date**: Thursday, Nov. 19, 2015
* **Time**: 12:00-1:00
* **Place**: East Conference Room
* **Presenter(s)**: Sudha Veturi
* **Topic(s)**: Genetic correlation for quantitative human traits
* **Materials:**:
* [Article](http://biorxiv.org/content/early/2015/01/27/014498)
* [Slides](https://sudhaveturi.shinyapps.io/LabMeeting)
--------------------------------------------
### Ideas for articles
If you have a paper you would like to present, use that one, otherwise feel free to choose one from this list
* [Fan et al. (Functional Linear (Meta) Analyses)](http://www.genetics.org/content/200/4/1089.full.pdf+html)
* [Bryc et al. (Ancestry in the US)](The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States)
* [ 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).
* [Gerstberger, et al., Protein-binding RNA](http://www.nature.com/nrg/journal/v15/n12/full/nrg3813.html).
* [Lu et al. high-throughput analysis of gene effects ] (http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg4008.html)
* [ Jiang et al. (Misspecified Mixed Models)](http://arxiv.org/abs/1404.2355 ) [did we discuss it last Fall?]
* [ Yang et al. (Mixed model assoc. analyses)](http://www.nature.com/ng/journal/v46/n2/full/ng.2876.html).
* Random Regressions: [Meyer (1997)](http://www.biomedcentral.com/content/pdf/1297-9686-30-3-221.pdf), [Kirkpatrick & Meyer (2004)](http://www.genetics.org/content/168/4/2295.short).