Multivariate adaptive shrinkage improves cross-population transcriptome prediction

2023-02-28 Daniel Araujo
𝔻ownload prediction weights from: Preprint from Wheeler lab sharing multi-ancestry prediction models from TOPMED/MESA […] Multivariate adaptive shrinkage improves cross-population … Read more →

How to map introns to genes

2023-02-22 Haky Im
𝔽ind the mapping from intron ids to gene ids in this link […] Q: How should I interpret the z-score? Does a negative z-score for an intron imply that a decrease in the excision of that intron leads to an increase in the GWAS trait? … Read more →

Protein prediction models - ARIC

2022-11-14 Sabrina Mi
𝔸RIC protein prediction models in predictdb format can be downloaded from here See more details here Read more →

MetaXcan output file formats

2022-03-08 Festus
𝕋he MetaXcan Software hosts a suite of tools i.e PrediXcan, SPrediXcan, MultiXcan and SMultiXcan. This post describes the file format output from each tool. […] Individual-level data method to compute gene-trait associations. Detailed info The output is a tab delimited file which contains … Read more →

Protein prediction for trait mapping in diverse populations

2022-02-12 Ryan Schubert, Heather Wheeler
ℙrediXcan ready databases and covariance files of the paper “Protein prediction for trait mapping in diverse populations” can be downloaded from here Read more →

Error for region (...) LinAlgError('SVD did not converge')

2021-07-23 PredictDB Team
𝕆ne step of the summary imputation, the computation of snp covariance matrix inverse, is performed via singular value decomposition (SVD). Numerical solutions to the SVD algorithm are not guaranteed to converge, and fail on some regions. When this happens, unmeasured zscores will not be present in … Read more →

Error No intersection between model names in MetaXcan Results and Prediction Models

2021-07-23 Festus
𝕋his error happen when the strings captured from the metaxcan results and models don’t coincide A good example is when the metaxcan results' captured names looked like Aorta while the models' captured names looked like Artery_Aorta, this will result into this error […] … Read more →

BrainXcan Brain Feature Prediction Models

2021-07-22 Yanyu Liang
𝕊-BrainXcan takes GWAS as input and return the association between GWAS phenotype and a list of brain image-derived phenotypes. BrainXcan manuscript link. Software documentation (Quick start) link. BrainXcan database link. Analysis scripts link. […] The software is built upon both Python and … Read more →

I need help and these FAQ doesn't cover my issue!

2021-07-21 PredictDB Team
𝔸: You can ask questions at the Google Group: Read more →

AttributeError 'NoneType' object has no attribute 'groups'

2021-07-21 Festus
𝕋his error happens when using the Multixcan tool, it usually happens when the tool cant find files in the Metaxcan folder you provided. Thus halting the process of meta analyzing the results. The most probable cause of this error are; […] –metaxcan_filter … Read more →