Public Notes

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

query alpha-missense

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

new test

TODO: delete this test post

testing quarto post app

test

You can install the development version of quartopost from GitHub with

Attenuation bias in PrediXcan

Uncertainty in predicted expression causes attenuation bias, and reduced significance of the association. Hence significance is underestimated.

qqunif function with filtered p-values

expected under the null is (1:nn) * maxp / (nn+1)

How to read gencode gtf file

analysis

how_to

to load version 75 of ensembl

Cistrome DB data

ERAP2 fine-mapping

analysis

how_to

ERAP2 fine-mapping results DAPG

Multiple Testing Vignette

vignette

We start defining some parameters for the simulations. The need for these will become obvious later.

Jane Austen Corpus

analysis

how_to

gtex-sample-size-by-tissue

GTEx Sample Size by Tissue

Migrating

how_to

Here will come the list of migrating instructions

PredictDB weight distribution

analysis

Goal: get effect size distribution of omic traits

Power calculator for mol QTLs

how to

The success of the prediction training depends mostly on…

How to create a new quarto blog post

how_to

Useful tips for new posts here

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

PARG Fall Social 2022

analysis

not very helpful, better to have list to select from rather than free text next time

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

How to annotate genes - BioMart Basics

cheatsheet

BioMart is a database containing…

Transcriptome QGT Lab 2022 Setup

The instructions in this blog were written to set up the lab in Rstudio cloud

Transcriptome QGT Training 2023

Notice that we may ask you to share your screen for pedagogic purposes.

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.

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

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.

Publishing a ShinyApp

First, we need to install and load the rsconnect package.

Biobank Japan Data in CRI

BBJ data directory: \gpfs/data/im-lab/nas40t2/Data/BBJ

ARIC PWAS models

The ARIC model for MetaXcan is in Box: https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc

ARIC EA hg38 validation

::: {.container-fluid .main-container} ::: {#header .fluid-row} # psychencode_hg38_validation {#psychencode_hg38_validation .title .toc-ignore}

ARIC EA hg38 validation height

::: {.container-fluid .main-container} ::: {#header .fluid-row} # ARIC EA validation {#aric-ea-validation .title .toc-ignore}

ARIC PWAS models

The ARIC model for MetaXcan is in Box: https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc

Covariances EA hg38

::: {.container-fluid .main-container} ::: {#header .fluid-row} # covariances_hg38 {#covariances_hg38 .title .toc-ignore}

Weights AA

::: {.container-fluid .main-container} ::: {#header .fluid-row} # generate weights {#generate-weights .title .toc-ignore}

Weights EA

::: {.container-fluid .main-container} ::: {#header .fluid-row} # generate weights {#generate-weights .title .toc-ignore}

Japan Biobank Data Summary (closed)

We have access to dataset JGAS000114 from the Biobank Japan Project. This includes:

Installing R packages without admin access

how to

** Note that this content was copied from the Berkely Statistics Website Original article linked here

Berkely Statistics

How to annotate a gene with the cytogenetic band

how to

Adding the cytogenetic to genes is convenient…

Tracking the traffic to webpages

how_to

To keep track of traffic to blogdown (hugo-based) webpages in google analytics, follow the steps below

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

Get list of predictor SNPs and weights in predictdb

how_to

To get a list of SNPs and the corresponding weights to…

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…

Mount Gardner file stystem to your computer

how to

Links to How To’s

how_to

Yanyu’s notes on uploading to zenodo

Training Gene Expression Prediction Models

how_to

PrediXcan and TWAS methods in general correlate genetically predicted levels of gene expression traits with…

PredictDB Tutorial

Github Cheatsheet

cheatsheet

Note: older repos may have master as the main branch

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…

Subsetting HapMap3 SNPs

how_to

This is the readme of the codes here.

How to use CRI cluster

how_to

cri

gardner

Note: A shortcut to login your tarbell account, please follow the following instruction: How-to-set-up-SSH-keys-and-configure-custom-connection-options-for-your-SSH-Client

Installing Conda on CRI

installlation

CRI has versions of miniconda already downloaded through the…

Natasha Santhnam

Heritability Calculation

How to calculate Heritability using GCTA

Natasha Santhanam

Querying PredictDB sqlite databases

how_to

PredictDB databases are…

Bionimbus PDC

how_to

Reference: * https://www.opensciencedatacloud.org/support/ssh.html * https://www.opensciencedatacloud.org/support/2fa.html

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…

PsychENCODE Models

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

PrediXcan 0% variant mapping issue

Many users had difficulties matching the genotype variant id to the prediction model variant id.

How to interpret a p-value of 0

A p-value of zero should be interpreted as an extremely small positive value.

CRI Gardner upgrade news

news

Operating System Upgrade - The operating system will be upgraded…

Working with Large Files

When working with large datasets, only the files with code should be pushed to Github repositories, not…

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

Installing/Running Tensorqtl on CRI

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

Creating Environments in CRI

Natasha Santhanam

Installing tensorqtl module

installlation

Installing tensorqtl requires pytorch which is based on gpus but there is also a cpu based version.

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.…

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.

Natasha Santhanam

Exploration on regressing out PCs

Some going-to-nowhere exploration on regressing out PCA

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.

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.

gwas-catalog

in 2020 [1] 94664 3

How to Prepare a Post Implementation Report?

how_to

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…

How to Use AWS

how_to

Stop/start your EC2 instances programatically through AWS Command Line Interface (CLI).

How to Submit to Zenodo

how_to

How to submit data to Zenodo

How to Use Workflowr

how_to

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

How to Configure Custom SSH Connection

how_to

This wiki will show you how to set up SSH keys and…

Molecular data available in GDC

how_to

How to Use RCC Cluster

how_to

https://rcc-uchicago.github.io/user-guide/

Downloading Data from Biobank Japan

how_to

The same info can be found at this…

Querying BigQuery

how_to

find examples here https://hakyimlab.github.io/bigquery-covid19/query-phenomexcan.html

Hands-On Training: plink

how_to

LATEST VERSION IN https://bios25328.hakyimlab.org/post/2021/04/07/plink-tutorial/

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…

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.

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…

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.

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…

GWAS on ANL Servers

how_to

Steps to running the GWAS on ANL’s servers.

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…

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.

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

Iris prediction with neural network

iris dataset analysis

test

other text here