𝕤interactive GCTA tutorial We’ll follow the GCTA tutorial here Read more →

ℝeview of maximum likelihood estimation […] Review of logistic regression […] Learn the basics of the command line […] Learn the basics of R […] Get Rstudio and the command line set up […] … Read more →

ℂreated by Yanyu Liang, with some material adapted from Charles Washington III and Jiamao Zheng’s lab 6 from 2018 As we know that eQTL analysis needs to test association for each gene in transcriptome against a set of variants. Typically, for cis-eQTL analysis, one gene could have thousands of … Read more →

ℂreated by Max Winston; modified by Charles Washington III, Ankeeta Shah, and Yanyu Liang This class is designed to introduce a variety of concepts, methods, and tools utilized in statistical genetics. The majority of tools used to employ these methods and concepts require basic knowledge of … Read more →

𝕋o recap, S-PrediXcan analysis takes GWAS summary statistics, gene expression prediction models (weights for SNPs), and reference LD and provides gene-level association between predicted expression and trait. So, it requires the following three pieces of data: […] The complete analysis … Read more →

𝕋his Lab will cover the quality batch portion of the QC and will be using the 1_Main_scripts_QC_GWAS.txt from Marees et al A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis. […] We will follow the tutorial published here by Marees et al A … Read more →

𝕀f you work on Midway2, some of the steps have been done for you (checked squares) […] # define environmental variables for convenience USERNAME="WRITE YOUR USER NAME HERE" PRE="/project2/bios25328/Data/Lab-QGT/" … Read more →

ℂreated by Max Winston & Brandon Pierce; modifications by Charles Washington III, Ankeeta Shah, and Yanyu Liang. Genome-wide Complex Trait Analysis (GCTA, see documentation here) was originally designed to estimate the heritability of complex traits using genome-wide SNPs, but has now been … Read more →

𝕎e will follow the tutorial published here by Marees et al A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis See the README file of the tutorial here […] If you want to work on the cluster you will need to load plink module avail ##Step 1 … Read more →

ℂreated by Max Winston, modified by Charles Washington III, Ankeeta Shah, and Yanyu Liang (from HGEN47100 course material) Before getting started, please download data from the Box link here. For your convenience, we have a copy of the data folder at /project2/hgen47100/data/lab2 on midway. wget … Read more →