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.
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READMEPrediction weights and covariance filesThe prediction weigths are saved in SQLite format, SearchThe Search option in the menu may be the fastest way to find the right models or answers to your questions. If you still have more questions, join our mailing list and post your questions there. You can also navigate through the menu options. Mailing ListPlease join our Google Group for general discussion, notification of future changes to our tools, feature requests, etc. DisclaimerThe models are provided “as is”, with the hope that they may be of use, without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. in no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the models or the use or other dealings in the models. References
LicenseThis work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. |
Ratxcan brain prediction models
2024-02-28
Haky Im
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 …
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Alpha-Missense Pathogenicity Query
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) …
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Multivariate adaptive shrinkage improves cross-population transcriptome prediction
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 …
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How to map introns to genes
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? …
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Protein prediction models - ARIC
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/
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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 …
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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
https://doi.org/10.5281/zenodo.4837327
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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 …
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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
[…] …
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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 …
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