MSBB brain alternative splicing QTL#
Contact#
Minghui Wang
Links to QTL analysis notebooks#
See notebooks in:
The notebooks in this folder contain the commands and data wrangling codes for analysis of the expression data in MSBB. (data wrangling exist because not all data are processed using the xqtl-pipeline from the beginning and need to be reformatted to fit one intermediate step of the pipeline).
Association data preprocessing#
Genotype data preprocessing#
Principal component analysis for eQTL mapping#
Phenotype data preprocessing#
Covariate data preprocessing#
Association scan using TensorQTL and summary statistics standardization#
Path(s) to cis-QTL association testing#
output of TensorQTL.ipynb
s3://statfungen/ftp_fgc_xqtl/analysis_result/cis_association/MSBB/sQTL/
Path(s) to fine-mapping with SuSiE RSS model#
Fine-mapping model objects (SuSiE-RSS, .rds) are available in the finemapping models folder (syn69670592).
Path(s) to TWAS models#
Pre-trained TWAS weight models for this context: syn69670600
Quantile TWAS (qTWAS) models: syn69670611
Path(s) to colocalization with SuSiE-coloc / ColocBoost#
Multi-context colocalization models (ColocBoost): syn69670597
AD GWAS–xQTL colocalization results: syn69865816
AD GWAS–xQTL colocalization models: syn69670630