Comments (8)
Hello Ioanna,
You are correct: currently there is no support for eQTL summary statistics as input for PrediXcan or MetaXcan. However, we are working on a tool that will allow you to obtain prediction models for gene expression in the format accepted by both programs (SQLite databases), from summary eQTL data (precisely what you are needing here). I happen to be working on this project at the moment, and hope to have some working code within a few weeks. If you are interested, I can contact you then, so you can generate models based on Blueprint eQTL summary statistics.
Best,
Rodrigo
from metaxcan.
Excellent, I am very much interested, please contact me once you are ready. Many thanks!
from metaxcan.
Dear Rodrigo,
I was wondering if there was any progress in your work on extending MetaXcan/PrediXcan to work with eQTL summary statistics? i am very keen to use it very soon for a manuscript I am preparing. Many thanks.
Best,
Ioanna
from metaxcan.
Dear Ioanna,
Yes, we'll have a first version of the tool released as a web application, really soon. You'll be able to upload your eQTL summary statistics files and get the prediction models and the covariance matrices (needed for MetaXcan) as output. We expect to have this first version within one week, hopefully. Thanks for your interest!
Best,
Rodrigo
from metaxcan.
Excellent, thank you.
from metaxcan.
Hi Rodrigo,
Do you have any updates please? :-)
Ioanna
from metaxcan.
Hi Ioanna,
I am sorry for not reaching back earlier, but unfortunately the release of the web app got delayed, however I have some scripts in a public GitHub repository that you can use to do the conversion (this). Since they are not documented yet, I just sent you an e-mail so I can help you use them for your particular data.
Best,
Rodrigo
from metaxcan.
Closing due to inactivity, assuming it fixed.
from metaxcan.
Related Issues (20)
- Question to SMulTiXcans pvalue HOT 2
- Create predictcan model from eQTL sum statistics
- MLE_did_not_converge
- Variants and genes in the mashr_Brain_Spinal_cord_cervical_c-1.db HOT 1
- The variant_id in GWAS Summary data can be CHR:POS:REF:ALT instead of rsid HOT 4
- Predict.py with imputation data HOT 4
- Error in installing MetaXcan and creating the environment in the LISA SURFSARA system HOT 1
- Problem creating covariance for s-mutlixcan HOT 1
- Problems with input data HOT 3
- How does PrediXcan with mashr model deal with missing genotype?
- Good meta-analysis method after predixcan HOT 1
- Only running 3 genes when using files I just pulled from PredictDB
- Very few SNPs used when using Michigan imputed data
- Too slow for calculating the expression level Tg
- S-MultiXcan results files - not all genes from individual tissues present HOT 2
- S-MultiXcan: extracting exact z-scores used to compute p-values (for p < e-324) HOT 3
- heritability estimates of gtex-v8 genes
- Requesting help:about QTL_to_PredictDB: AttributeError: 'NoneType' object has no attribute 'endswith'
- issue while running SMulTiXcan.py. AttributeError: 'Series' object has no attribute 'zscore' HOT 2
- MASHR-based GTEx v8 gene expression models
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from metaxcan.