Knight ADRC brain gene expression QTL
Access
Controlled access. Request data access for Knight-ADRC on the AD Knowledge Portal; you need a Synapse account. See How to get the data.
| Where | ID | Access | What you get |
|---|---|---|---|
| Synapse | syn69670592 | Controlled | Results described below |
Other Synapse IDs on this page syn69670600 syn69670611 syn69670597 syn69865816 syn69670630
pip install synapseclient
synapse login
synapse get -r syn69670592Contact
Chunming Liu
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 KnightADRC. (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
Knight_data_RNASeq.ipynb shows the commands used for phenotype calling.
genotype_preprocessing.ipynb shows the commands used for genotype processing and preparation steps.
phenotype_preprocessing.ipynb shows the commands used for the phenotype data processing and preparation steps.
covariate_preprocessing.ipynb shows the commands used for the covariate data processing and preparation steps.
Association scan using TensorQTL and summary statistics standardization
- TensorQTL.ipynb provides the pipeline to generate TensorQTL cis association results for all QTLs.
- Knight_eQTL_commands provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1].
Path(s) to cis-QTL association testing
output of TensorQTL.ipynb
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
Analyses
- cis-QTLDone
- SuSiEDone
- TWASDone
Read from the methods: map in this page's metadata header, the same data as the analysis coverage grid.