PredictDB Data Repository
Here you can find transcriptome and other traits prediction weights for the PrediXcan family of methods: S-PrediXcan, MultiXcan, S-MultiXcan, and BrainXcan.
Prediction weights and covariance files
The prediction weigths are saved in SQLite format,
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2023-11-13 Haky Im
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 →
2023-02-28 Daniel Araujo
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 →
2023-02-22 Haky Im
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 →
2022-11-14 Sabrina Mi
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 →
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 https://doi.org/10.5281/zenodo.4837327 Read more →
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 →
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 →
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 →
2021-07-21 PredictDB Team
𝕋he prediction model databases only contain models that pass a stringent criteria (each family of models has its own criteria, e.g. MASHR models require at least one snp with high posterior probability of being an eQTL). Our model training algorithms are complex and conservative. Sometimes, a good … Read more →