Hands-On Training: plink

𝕃ATEST VERSION IN […] A more detailed tutorial for GWAS analysis is here. […] We will learn to run a GWAS using plink. This tutorial follows a plink tutorial you can find here […] … Read more →

Using R_Markdown

2020-07-08 Ian Waters
ℝ Markdown is a authoring framework that allows for reproducible documentation of data science within the context of R Studio. This is an introduction designed to teach you how to use R Markdown in a few minutes. Further info and some of the examples used below can be found here: … Read more →

Hands-On Training: R

2020-07-05 Laura Vairus
𝕊wirl is a great and easy way to get you started with R. Install and open it by clicking the green arrow on the right. Install Swirl Package: install.packages("swirl") library("swirl") swirl() Once you enter your username, it prompts you to choose a course to install. Choose 1 … Read more →

Hands-On Training: Command Line

2020-07-02 Laura Vairus
𝕀n this tutorial, we will learn some basic Unix/Linux commands to perform tasks in the command line. The command line is an interface that allows you to store, manage, and process data. Terminal is an app that gives you access to the command line. (Note: This tutorial was made for Mac users. For … Read more →

Converting Fusion weight to PredictDB format

2020-06-22 Sabrina Mi
𝕀f you want to use the MetaXcan suite of tools, you will need to format your prediction weights in sqlite format. Find a sample script that formats FUSION weights to predictdb format here If you want to use the summary version of PrediXcan, you will also need the covariances between SNPs Fine a … Read more →

IntroStatGen R Studio Servers using Google Cloud

2020-06-16 Owen Melia
𝔽or the one-day seminar, we had a hands-on lab where we decided we needed to set up R Studio Servers. The servers needed pre-loaded data, access to a terminal, pre-compiled binaries for torus and fastenloc, and the correct python/R/Linux environments to run all of our analyses. Here’s a guide … Read more →

Test of something normal

2004-10-30 Haky Im
𝕋his is a histogram of 1000 independent normal random variables. yy = rnorm(1000) hist(yy) I prefer more bins for the histogram hist(yy, 50) xx = rnorm(1000) plot(xx,yy) Read more →

dbGaP Project Renewal

𝕋he email reminder to renew dbGaP projects should link to My Projects tab after logging in, where you can select the project to request renewal. For the most part, the application will walk through the steps if you click ‘save and continue’ at the bottom of each page, but there are tabs … Read more →

GWAS on ANL Servers

𝕊teps to running the GWAS on ANL’s servers. […] This was done by Tom Brettin. Hail is working on the nucleus machine, but not washington at the moment. […] Downstream analysis can be a lot faster with a smaller genetic dataset. We filtered for individuals in the brain imaging … Read more →

How to Download the Data from the UK Biobank

𝔸pplication 19526 is the main application from which imlab downloads data. Other ID’s correspond to specific collaborations with other investigators at Uchicago and Argonne. We have requested data in 8 baskets, with overlapping fields. The composition of the baskets are somewhat haphazard, they were … Read more →