IM Lab Notebook

This is a public notebook with analysis bits, how to’s, and other notes from the hakyimlab members.

To add new posts, check these instructions

Click here for the lab’s internal notebook’s repo or here for the internal notebook’s website for draft material not ready for sharing publicly

ARIC PWAS models

2021-09-08 Sabrina Mi
𝕋he ARIC model for MetaXcan is in Box: https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc […] The Atherosclerosis Risk in Communities Study (ARIC) generated genotype and proteomic data from a total of 9,084 participants (7,213 European Americans and 1,871 African Americans). The … Read more →

Japan Biobank Data Summary

2021-08-12 Sabrina Mi
𝕎e have access to dataset JGAS000114 from the Biobank Japan Project. This includes: […] See list of phenotypes and more details here Read more →

Installing R packages without admin access

2021-07-29 Berkely Statistics
** Note that this content was copied from the Berkely Statistics Website Original article linked here Library Path Management First, note that in general, the administrators of the High Performance Computing clusters will install an R package on the system. However, you can also install packages … Read more →

How to annotate a gene with the cytogenetic band

2021-07-28 Haky Im
𝔸dding the cytogenetic to genes is convenient because it provides a somewhat memorable names for the genomic region where the gene is located. Biomart package in bioconductor has the database and function for the annnotation. suppressMessages(library(tidyverse)) suppressMessages(library(glue)) … Read more →

Tracking the traffic to webpages

2021-07-26 Haky Im
𝕋o keep track of traffic to blogdown (hugo-based) webpages in google analytics, follow the steps below See Google’s instructions here. Briefly […] Copy the global site tag, which is several lines of code that you need to paste into each webpage you want to measure. Below is the code for … Read more →
FAQ

Error: 0 % SNPs used

2021-07-20 Festus
𝕄ismatch between the model SNP ids and geneotype/gwas SNP ids, e.g using model rsids to match with genotype variant_ids […] When having different genome builds use chr{}{}{}_{}_b38" for the –on_the_fly_mapping argument. This parameter specifies a format string to be used when … Read more →

Get list of predictor SNPs and weights in predictdb

2021-07-19 Haky Im
𝕋o get a list of SNPs and the corresponding weights to predict expression levels (or splicing) of a given gene, you will first need to download the databases where the prediction models are stored. For example, you can download them from here more specifically from this tar file On CRI they are … Read more →

Download LD blocks

2021-07-13 Festus Nyasimi
𝕋his is a short tutorial on how to download ld block data as summarized by Berisa and Pickrell. The LD data is available in hg19 genome build and for three different populations i.e. AFR, ASN and EUR. First download the data from the bit bucket repository git clone … Read more →

Links to How To's

2021-07-12 Haky Im
𝕐anyu’s notes on uploading to zenodo Read more →

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 →