ℙrediXcan and TWAS methods in general correlate genetically predicted levels of gene expression traits with complex traits to understand the mechanism behind GWAS loci. A key component is the training of gene expression traits. A tutorial on how to generate elastic net models can be found in this … Read more →

𝕋his tutorial will provide the steps you need to follow to get you started training prediction models and putting them in a format that can be used to run the predixcan suite of software. […] The training dataset can be downloaded from this link.The data set includes the following files you … Read more →

ℍands on exercises for the QGT workshop 2021 can be found here Read more →

𝕋o publish an analysis note in the notebook, you need to have blogdown and hugo installed on your computer. […] When running analysis, data should be placed in Box not under the githup repo. Add block as shown in the next block, which will automatically create a folder with the same name in … Read more →

-- Remove the history from rm -rf .git -- recreate the repos from the current content only git init git add . git commit -m "Initial commit" -- push to the github remote repos ensuring you overwrite history git remote add origin https://github.com/<YOUR ACCOUNT>/<YOUR … Read more →

𝕋his is the readme of the codes here. This module extract HapMap 3 SNPs for downstream use. Download data from https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3_r3/plink_format/ The workflow is based on snakemake and it contains the following steps: […] If one wants to do liftover, then … Read more →

ℕote: A shortcut to login your tarbell account, please follow the following instruction: How-to-set-up-SSH-keys-and-configure-custom-connection-options-for-your-SSH-Client […] Please follow the instructions to access /gpfs/data/im-lab/ from the University of Chicago’s Network: … Read more →

ℂRI has versions of miniconda already downloaded through the module commands. However, those sometimes do not work so it is best to just install conda for yourself on CRI. The whole process is quite simple and should only take a few minutes. First download the conda installer from their website You … Read more →

ℍow to calculate Heritability using GCTA If you’re data is already in a PLINK form then it’s quite easy to use GCTA. You need to first create the genetic relatedness matrix (GRM) - make sure you’ve already done quality control on the genotype data since a high rate of missing SNPS … Read more →

ℙredictDB databases are stored in simple sqlite files. You can programmatically query them via python, R, perl, etc (using appropriate libraries). Below is an example on how to query the database in R. Each has two tables the extra and the weights tables. - extra table contains the list of available … Read more →