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Welcome to the website for the Summer Institue in Statistical Genetics module: Association mapping and Sequencing.
Instructors: Loic Yengo & Joelle Mbatchou
You will find on this website link to lecture slides, exercises including some solutions, and link to the class video recordings.
The module has 10 sessions, each of 80 minutes. The standard format for a session is approximately:
We will cover a total of 8 sessions split between July 25-27th. The tentative course schedule is below.
Prior to the module, please install up-to-date versions of: * R (Version 4.1+): available from this list of sites * RStudio (Version 1.4+): available here * PLINK (Version 1.9): available here * PLINK (Version 2.0): available here * REGENIE (Version 3.1.1+): available here
All four are free software. REGENIE requires MAC/Linux system; if you have a Windows laptop, you can install docker to setup a Linux image (see here).
The following R packages from CRAN will be used and should be installed prior to the module: * qqman The R commands below can be used to install the CRAN R package:
install.packages("qqman")This is a tentative schedule. All times listed below for the schedule are Eastern Standard Time (EST).
All individual data files below can be downloaded from two zipped folder from dropbox. This files can be downloaded here:
Alternatively, you can download each of the data files in the Github repository.
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 rstudioapi_0.13 knitr_1.31 whisker_0.4
[5] magrittr_1.5 getPass_0.2-2 R6_2.4.1 rlang_1.0.1
[9] fastmap_1.1.0 stringr_1.4.0 httr_1.4.3 tools_3.6.1
[13] xfun_0.31 cli_3.1.1 jquerylib_0.1.4 git2r_0.30.1
[17] htmltools_0.5.2 yaml_2.2.1 digest_0.6.25 rprojroot_2.0.3
[21] tibble_2.1.3 crayon_1.3.4 processx_3.5.3 callr_3.7.0
[25] later_1.3.0 sass_0.4.0 promises_1.2.0.1 fs_1.5.2
[29] ps_1.7.0 glue_1.6.1 evaluate_0.14 rmarkdown_2.14
[33] stringi_1.4.6 bslib_0.3.1 pillar_1.4.3 compiler_3.6.1
[37] jsonlite_1.7.2 httpuv_1.6.5 pkgconfig_2.0.3