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FunGen-xQTL Computational Protocol

Getting started

Environment Setup
xQTL Analysis Workflow Builder

Reference data

Reference data preparation

Molecular Phenotypes

RNA-seq expression
Single-cell and single-nucleus molecular phenotype preprocessing
- snRNA-seq Preprocessing
- Single-nuclei Pseudobulk Preprocessing (RNA-seq and ATAC-seq)
DNA methylation preprocessing
- Quantification of methylation data
Alternative splicing from RNA-seq data
- Quantifying alternative splicing from RNA-seq data
- Splicing QC and Normalization
Alternative polyadenylation
- APA Calling
- Post-APA calling: Imputation and QC

Data Preprocessing

Genotype preprocessing
Phenotype preprocessing
Covariate data preprocessing
- Covariate Data Formatting
- Hidden Factor Analysis

QTL Association Testing

QTL association testing
- QTL Association Testing (TensorQTL)
- Quantile regression for QTL association testing
Hierarchical Multiple Testing

Multivariate Mixture Models

Multivariate adaptive shrinkage (MASH) mini-protocol

Multiomics Regression Models

Fine-mapping and TWAS analysis
Fine-mapping result post-processing

GWAS Integration

GWAS and xQTL integration mini-protocol

Enrichment and Validation

Enrichment and functional validation mini-protocol

xQTL Modifier Score

scEEMS Model Training
scEEMS Prediction

About

Contributors

Index

By The NIH/NIA Alzheimer's Disease Sequencing Project Functional Genomics xQTL Consortium

© Copyright 2021+, FunGen xQTL Analysis Working Group.