𝔾iven the pervasive polygenicity of most complex traits, we found that TWAS results can be substantially inflated, yielding many more false positives than expected. We describe the problem and solution in this preprint. We updated the MetaXcan software and prediction models to correct for this … Read more →

𝕊ee description in CITE scPredixcan PAPER HERE See github reo in scPrediXcan github repo Download models here from Box folder or from Zenodo (for islet cells from T2D dataset) and Zenodo (for immune cells from OneK1K dataset). […] As scPrediXcan is a newly-developed tool, there may be some … Read more →

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ℙrediction models of five brain region gene expression in rats. See description in Santhanam, Sanchez Roige, et al (2024). Download link To query the database, checkout this post […] Natasha Santhanam, Sandra Sanchez-Roige, Yanyu Liang, Apurva S. Chitre, Daniel Munro, Denghui Chen, Riyan … Read more →

𝕎e downloaded the pathogenicity predictions from Alpha-Missense and made this shinyapp to query. Try it out. https://imlab.shinyapps.io/alphamissense-query-hugo/ Jun Cheng et al., Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 381 (2023) … Read more →

𝔻ownload prediction weights from: https://zenodo.org/record/7551845#.Y_5QTLTMIqs Preprint from Wheeler lab sharing multi-ancestry prediction models from TOPMED/MESA https://www.biorxiv.org/content/10.1101/2023.02.09.527747v1 […] Multivariate adaptive shrinkage improves cross-population … Read more →

𝔽ind the mapping from intron ids to gene ids in this link https://uchicago.box.com/s/xy71r0su6refrfggivrwc7kpvsxysmmn […] 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 →

𝔸RIC protein prediction models in predictdb format can be downloaded from here https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc See more details here https://lab-notes.hakyimlab.org/post/2021-09-08-generating-metaxcan-prediction-model-from-aric-pwas/ Read more →

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 →

ℙrediXcan ready databases and covariance files of the paper “Protein prediction for trait mapping in diverse populations” can be downloaded from here https://doi.org/10.5281/zenodo.4837327 Read more →