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

How to prepare effective presentation slides

2022-11-30 Haky Im
ℂitation: Naegle KM (2021) Ten simple rules for effective presentation slides. PLoS Comput Biol 17(12): e1009554. https://doi.org/10.1371/journal.pcbi.1009554 Published: December 2, 2021 Copyright: © 2021 Kristen M. Naegle. This is an open access article distributed under the terms of the Creative … Read more →

PARG Fall Social 2022

2022-10-20 Haky Im
𝕤uppressMessages(library(tidyverse)) suppressMessages(library(glue)) PRE = "/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data" ##PRE="/Users/margaretperry/Library/CloudStorage/Box-Box/imlab-data/data-Github/web-data " … Read more →

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 https://github.com/sabrina-mi/ukbrest The standard ukbREST setup involves loading UKB CSVs into a … Read more →

How to annotate genes - BioMart Basics

2022-06-28 Sabrina Mi
𝔹ioMart is a database containing Ensembl annotations of genes across many species and builds. To query data, you first pick one the databases: […] We typically uses only the Ensembl Genes database, which lists all genes for the selected species and build, along with their positions, alternate … Read more →

Transcriptome QGT Lab 2022 Setup

2022-06-14
𝕋he instructions in this blog were written to set up the lab in Rstudio cloud […] Linux is the operating system of choice to run bioinformatics software. You will need either a computer running linux or or mac os, which has a linux-like environment. […] #install R packages … Read more →
Lab

Transcriptome QGT Training 2022

2022-06-10 Haky Im
𝕎e ask you to actively participate in today’s hands on activities. Notice that we may ask you to share your screen for pedagogic purposes. […] If you have any concerns about this, please ask me or one of the TAs for assistance. We are here to help you learn. […] After each section, we … 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 →

How-to-open-jupyter-notebook-on-CRI-or-RCC

2022-05-17 Charles Zhou
𝕋his is a workflow to show how to open jupyter notebook on CRI or RCC. There are some detailed instructions here, CRI’s instructions and More general instructions […] https://rcc.uchicago.edu/docs/software/environments/python/index.html#running-jupyter-notebooks […] log into … Read more →

Publishing a ShinyApp

2022-03-07 Ethan Tai
𝔽irst, we need to install and load the rsconnect package. install.packages('rsconnect') library('rsconnect') Once you login to shinyapps.io, navigate to the token page. Then, we can access our own personal token, which we need to link to our RStudio session, by clicking show, show secret, and … Read more →

Biobank Japan Data in CRI

2022-01-02 Sabrina Mi
𝔹BJ data directory: \gpfs/data/im-lab/nas40t2/Data/BBJ I first downloaded and decrypted Biobank Japan data (instructions), then organized into subdirectories BBJ-genotypes-decrypted and BBJ-phenotypes-decrypted, in their original form. […] BBJ phenotypes file: … Read more →