Public Notes

Now generated with quarto. Add or edit posts on github here

compare ratxcan with and without loco

compare ratxcan mixed effects with and without loco
Aug 29, 2024
Haky Im

 

how to apply to F30/31 grants

how-to

material collected by grad students at UChicago
Jul 11, 2024
Jennifer Blanc, Eric McIntire

 

recount quick access

how to quickview recount
May 31, 2024
Haky Im

 

bios25328 lab 1 command line and R

bios25328
lab
We will learn to use the command line by doing. Follow the instructions below.
Mar 18, 2024
Haky Im

how to run for loops in parallel in R

In this exammple, n~2e5 is the break even point, beyond which, the overhead of parallel computation is offset by the parallel computation
Feb 16, 2024
Haky Im

 

query alpha-missense

First, ensure SQLite3 is installed. If it’s not, you can install it using Homebrew on macOS:
Oct 23, 2023
Haky Im

 

How to create a new Quarto Blog

how_to

This is a tutorial on how to create a new quarto blog using the R studio interface
Sep 15, 2023
Sofia Salazar

 

new test

TODO: delete this test post
Aug 10, 2023
Haky Im

 

testing quarto post app

test
You can install the development version of quartopost from GitHub with
Aug 10, 2023
Haky Im

Attenuation bias in PrediXcan

Uncertainty in predicted expression causes attenuation bias, and reduced significance of the association. Hence significance is underestimated.
Jul 3, 2023
Haky Im

qqunif function with filtered p-values

expected under the null is (1:nn) * maxp / (nn+1)
Jun 16, 2023
Haky Im

 

How to read gencode gtf file

analysis
how_to
to load version 75 of ensembl
Apr 27, 2023
Haky Im

 

Cistrome DB data

Mar 28, 2023
Haky Im

ERAP2 fine-mapping

analysis
how_to
ERAP2 fine-mapping results DAPG
Mar 28, 2023
Haky Im

Multiple Testing Vignette

vignette
We start defining some parameters for the simulations. The need for these will become obvious later.
Mar 28, 2023
Haky Im

 

Jane Austen Corpus

analysis
how_to
Mar 22, 2023
Haky Im

 

gtex-sample-size-by-tissue

GTEx Sample Size by Tissue
Mar 1, 2023
Haky Im

 

Migrating

how_to
Here will come the list of migrating instructions
Feb 28, 2023
Haky

PredictDB weight distribution

analysis
Goal: get effect size distribution of omic traits
Feb 28, 2023
Haky Im

 

Power calculator for mol QTLs

how to
The success of the prediction training depends mostly on…
Feb 21, 2023
Haky Im

 

How to create a new quarto blog post

how_to
Useful tips for new posts here
Jan 1, 2023
Haky Im

How to prepare effective presentation slides

how to
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
Nov 30, 2022
Haky Im

 

PARG Fall Social 2022

analysis
not very helpful, better to have list to select from rather than free text next time
Oct 20, 2022
Haky Im

 

ukbREST SQLite Setup

installlation
how to
This post explains how to 1. Query UKBREST in CRI 2. Create an SQLite database from the postgres database 3. Update the withdrawal list
Aug 28, 2022
Sabrina Mi

 

How to annotate genes - BioMart Basics

cheatsheet
BioMart is a database containing…
Jun 28, 2022
Sabrina Mi

 

Transcriptome QGT Lab 2022 Setup

The instructions in this blog were written to set up the lab in Rstudio cloud
Jun 14, 2022

Transcriptome-wide association methods

Transcriptome QGT Training 2023

Notice that we may ask you to share your screen for pedagogic purposes.
Jun 10, 2022
Haky Im

 

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

how to
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.
May 22, 2022
Charles Zhou

 

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

how_to
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
May 17, 2022
Charles Zhou

How to calculate Z-score, P-value, Chi2 stat from GWAS

Given one of the statistics in a GWAS (Z-score, P-value, or chi2), calculate the others.
Apr 13, 2022
Haky Im

Publishing a ShinyApp

First, we need to install and load the rsconnect package.
Mar 7, 2022
Ethan Tai

 

Biobank Japan Data in CRI

BBJ data directory: \gpfs/data/im-lab/nas40t2/Data/BBJ
Jan 2, 2022
Sabrina Mi

ARIC EA hg38 validation

::: {.container-fluid .main-container} ::: {#header .fluid-row} # psychencode_hg38_validation {#psychencode_hg38_validation .title .toc-ignore}
Sep 8, 2021
Sabrina Mi

ARIC EA hg38 validation height

::: {.container-fluid .main-container} ::: {#header .fluid-row} # ARIC EA validation {#aric-ea-validation .title .toc-ignore}
Sep 8, 2021
Sabrina Mi

 

ARIC PWAS models

The ARIC model for MetaXcan is in Box: https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc
Sep 8, 2021
Sabrina Mi

 

Covariances EA hg38

::: {.container-fluid .main-container} ::: {#header .fluid-row} # covariances_hg38 {#covariances_hg38 .title .toc-ignore}
Sep 8, 2021
Sabrina Mi

 

Weights AA

::: {.container-fluid .main-container} ::: {#header .fluid-row} # generate weights {#generate-weights .title .toc-ignore}
Sep 8, 2021
Sabrina Mi

 

Weights EA

::: {.container-fluid .main-container} ::: {#header .fluid-row} # generate weights {#generate-weights .title .toc-ignore}
Sep 8, 2021
Sabrina Mi

 

Japan Biobank Data Summary (closed)

We have access to dataset JGAS000114 from the Biobank Japan Project. This includes:
Aug 12, 2021
Sabrina Mi

 

Installing R packages without admin access

how to
** Note that this content was copied from the Berkely Statistics Website Original article linked here
Jul 29, 2021
Berkely Statistics

How to annotate a gene with the cytogenetic band

how to
Adding the cytogenetic to genes is convenient…
Jul 28, 2021
Haky Im

 

Tracking the traffic to webpages

how_to
To keep track of traffic to blogdown (hugo-based) webpages in google analytics, follow the steps below
Jul 26, 2021
Haky Im

 

Error: 0 % SNPs used

FAQ
Mismatch between the model SNP ids and geneotype/gwas SNP ids, e.g using model rsids to match with genotype variant_ids
Jul 20, 2021
Festus

 

Get list of predictor SNPs and weights in predictdb

how_to
To get a list of SNPs and the corresponding weights to…
Jul 19, 2021
Haky Im

 

Download LD blocks

how to
This is a short tutorial on how to download ld block data as summarized by Berisa and Pickrell. The LD data is…
Jul 13, 2021
Festus Nyasimi

 

Mount Gardner file stystem to your computer

how to
T…
Jul 12, 2021
Festus Nyasimi

 

Links to How To’s

how_to
Yanyu’s notes on uploading to zenodo
Jul 12, 2021
Haky Im

 

Training Gene Expression Prediction Models

how_to
PrediXcan and TWAS methods in general correlate genetically predicted levels of gene expression traits with…
Jul 9, 2021
Haky Im

 

PredictDB Tutorial

This…
Jun 28, 2021
Festus Nyasimi

 

Github Cheatsheet

cheatsheet
Note: older repos may have master as the main branch
Jun 16, 2021
Haky Im

Creating a new post (deprecated)

how_to
To publish an analysis note in the notebook, you need to have blogdown and hugo installed on your computer. - install.packages('blogdown') - blogdown::install_hugo() - git clone this repository…
Jun 16, 2021
Haky Im

 

Subsetting HapMap3 SNPs

how_to
This is the readme of the codes here.
Jun 14, 2021
Yanyu Liang

 

How to use CRI cluster

how_to
cri
gardner
this document needs updating. Here is a quick start guide for randi, which replaced gardner, decommissioned for a while now (2024-07-15)
Jun 10, 2021

 

Installing Conda on CRI

installlation
CRI has versions of miniconda already downloaded through the…
Jun 4, 2021
Natasha Santhnam

 

Heritability Calculation

How to calculate Heritability using GCTA
Jun 3, 2021
Natasha Santhanam

 

Querying PredictDB sqlite databases

how_to
PredictDB databases are…
Apr 27, 2021
Haky Im

 

Bionimbus PDC

how_to
Reference: * https://www.opensciencedatacloud.org/support/ssh.html * https://www.opensciencedatacloud.org/support/2fa.html
Mar 31, 2021
Sabrina Mi

 

SPrediXcan Harmonization Errors

The error message– INFO - 0 % of model's snps used– can typically be traced to inconsistencies between variant IDs in prediction models and input GWAS files. Our GTEx…
Jan 7, 2021
Sabrina Mi

PsychENCODE Models

Gandal et al analyzed autism spectrum disorder, schizophrenia, and bipolar disorder across multiple levels of transcriptomic organization—gene expression, local splicing…
Dec 21, 2020
Sabrina Mi

 

PrediXcan 0% variant mapping issue

Many users had difficulties matching the genotype variant id to the prediction model variant id.
Dec 1, 2020
Haky Im

 

How to interpret a p-value of 0

A p-value of zero should be interpreted as an extremely small positive value.
Dec 1, 2020
Haky Im

 

CRI Gardner upgrade news

news
Operating System Upgrade - The operating system will be upgraded…
Nov 30, 2020
Haky Im

 

Working with Large Files

When working with large datasets, only the files with code should be pushed to Github repositories, not…
Nov 23, 2020
Sabrina Mi

 

How to convert GTEx v8 model to hg19 based on UK Biobank SNP set mapping

/gpfs/data/im-lab/nas40t2/Data/References/mappings/UKB2GTEx_mapping.txt.gz contains information for variants in UK Biobank genotypes. The columns are
Nov 23, 2020
Sabrina Mi

 

Installing/Running Tensorqtl on CRI

Note: You can download tensorqtl using pip install. However, there seems to be a bug that makes tensorqtl…
Nov 17, 2020
Natasha

 

Creating Environments in CRI

Nov 13, 2020
Natasha Santhanam

 

Installing tensorqtl module

installlation
Installing tensorqtl requires pytorch which is based on gpus but there is also a cpu based version.
Nov 11, 2020
Festus Nyasimi

 

Querying bgen files in CRI

A bgen file has a header block with information about the file, including number of samples, the number of variant data blocks, and flags which describe how data is stores.…
Nov 10, 2020
Sabrina Mi

Calculating H2 across GTEX Brain Samples

After receiving a .RAR file with reaction rate data for 13 brain tissue samples, we wanted to calculate h2 and see if any of the thousands of reactions were heritable.
Nov 6, 2020
Natasha Santhanam

Exploration on regressing out PCs

Some going-to-nowhere exploration on regressing out PCA
Nov 4, 2020
Yanyu Liang

GTEx reaction rates h2 similar to permuted h2

We want to investigate whether reaction rates estimated with imat(?) are heritable. Reaction rates (binary variables) were estimated by D using GTEx gene expression data.
Nov 2, 2020
Haky Im

 

Configuring Windows Subsystem for Linux

how_to
This is a guide to configuring a Windows system to utilize many of the tools that the Im Lab uses.
Aug 10, 2020
Ian Waters

gwas-catalog

in 2020 [1] 94664 3
Aug 2, 2020
Hae Kyung Im

 

How to Prepare a Post Implementation Report?

how_to
This…
Jul 30, 2020

 

Computing on ANL Servers

how_to
To get access to the servers at ANL, you will need at minimum an account with Argonne’s MCS…
Jul 30, 2020

 

How to Use AWS

how_to
Stop/start your EC2 instances programatically through AWS Command Line Interface (CLI).
Jul 30, 2020

 

How to Submit to Zenodo

how_to
How to submit data to Zenodo
Jul 30, 2020

 

How to Use Workflowr

how_to
#Open RStudio
Jul 30, 2020

 

Downloading and Decrypting dbGaP Data

how_to
This page is about downloading and decrypting data from NCBI dbGaP. I will split up the instructions into Downloading and Decrypting
Jul 30, 2020

 

How to Configure Custom SSH Connection

how_to
This wiki will show you how to set up SSH keys and…
Jul 30, 2020

 

Molecular data available in GDC

how_to
Jul 30, 2020

 

How to Use RCC Cluster

how_to
https://rcc-uchicago.github.io/user-guide/
Jul 30, 2020

Downloading Data from Biobank Japan

how_to
The same info can be found at this…
Jul 30, 2020
Sabrina Mi

 

Querying BigQuery

how_to
find examples here https://hakyimlab.github.io/bigquery-covid19/query-phenomexcan.html
Jul 30, 2020

 

Hands-On Training: plink

how_to
LATEST VERSION IN https://bios25328.hakyimlab.org/post/2021/04/09/plink-tutorial/
Jul 14, 2020

Using R_Markdown

how_to
R Markdown is a authoring framework that allows for reproducible documentation of data science within the context of R Studio. This…
Jul 8, 2020
Ian Waters

 

Hands-On Training: R

how_to
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.
Jul 5, 2020
Laura Vairus

 

Hands-On Training: Command Line

how_to
In this tutorial, we will learn some basic Unix/Linux commands to perform tasks in the command line.
The…
Jul 2, 2020
Laura Vairus

 

Converting Fusion weight to PredictDB format

how_to
If you want to use the MetaXcan suite of tools, you will need to format your prediction weights in sqlite format.
Jun 22, 2020
Sabrina Mi

 

IntroStatGen R Studio Servers using Google Cloud

how_to
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…
Jun 16, 2020
Owen Melia

 

benjamin moore colors

Read benjamin moore list of colors with HEX code from colornerd
Jan 1, 2020
Haky Im

 

GWAS on ANL Servers

how_to
Steps to running the GWAS on ANL’s servers.
Jul 30, 2001

 

dbGaP Project Renewal

how_to
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…
Jul 30, 2001

 

How to Download the Data from the UK Biobank

how_to
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.
Jul 30, 2001

 

lego database

downloads schema in /Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data/2000-01-01-lego-database/downloads_schema.png
Jan 1, 2000
Haky Im

Iris prediction with neural network

Jan 1, 1999
Haky Im

iris dataset analysis

Jan 1, 1999
Haky Im

 

test

other text here
Jan 1, 1999
testing author
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