Posts

Mount Gardner file stystem to your computer

2021-07-12 Festus Nyasimi
𝕋his page contains description on how to map CRI storage to your computer. Depending on the operating system you are using there are different approaches. Which are shown below; […] sudo apt-get install sshfs Create the mount point # Create the mountpoint [festus@ubuntu ~ ]$ mkdir ~/im-lab … Read more →

Training Gene Expression Prediction Models

2021-07-09 Haky Im
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 →

PredictDB Tutorial

2021-06-28 Festus Nyasimi

Quantitative Genomics Training 2021

2021-06-22 Haky Im et al
ℍands on exercises for the QGT workshop 2021 can be found here Read more →

Creating a new post

2021-06-16 Haky Im
𝕋o publish an analysis note in the notebook, you need to have blogdown and hugo installed on your computer. […] Netlify is hosting the content here Read more →

Github Cheatsheet

2021-06-16 Haky Im
-- 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 git@github.com:<YOUR ACCOUNT>/<YOUR REPOS>.git … Read more →

Subsetting HapMap3 SNPs

2021-06-14 Yanyu Liang
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 →

How to use CRI cluster

2021-06-10
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 →

Installing Conda on CRI

2021-06-04 Natasha Santhnam
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 →

Heritability Calculation

2021-06-03 R package build
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 →