how to

ukbREST SQLite Setup

2022-08-28 Sabrina Mi
𝕋his post explains how to […] The version of ukbREST that runs on SQLite is HERE. If you come across an existing ukbrest repo in CRI, it might be the original version. […] git clone The standard ukbREST setup involves loading UKB CSVs into a … Read more →

How to query eqtl info from GTEx API (a simple way)

2022-05-22 Charles Zhou
𝕋his is a simple and convenient way to get some information about certain eqtls from GTEx API. But it may not be a good way to do big query because it’s not so fast. […] import requests import json import pandas as pd import time # if you want to measure the query speed Get … 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 →

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 →

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 →