KGGSEE doc

Contents:

• 1 Introduction
• 2 Installation
  • 2.1 kggsee.jar
  • 2.2 Resource data
• 3 Tutorials
  • 3.1 Gene-based association analysis
  • 3.2 Estimate the phenotype-associated cell-types of a phenotype (DESE)
  • 3.3 Conditional gene-based association analysis with eDESE
  • 3.4 Gene-based causality analysis
  • 3.5 Drug repositioning based on the drug selective perturbation analysis(SelDP)
• 4 Functions
  • 4.1 Gene-based association analysis by an effective chi-square statistics(ECS)
  • 4.2 Finely map genes and estimate relevant cell types of a phenotype by the single-cell (or bulk-cell) type and phenotype cross annotation framework(DESE)
  • 4.3 Multi-strategy Conditional Gene-based Association framework mainly guided by eQTLs (eDESE)
  • 4.4 Infer the causal genes based on GWAS summary statistics and eQTLs by Mendelian randomization analysis framework for causal gene estimation(EMIC)
  • 4.5 Compute the gene/isoform-level eQTLs of each tissue
• 5 Options Index
  • 5.1 Inputs/outputs
  • 5.2 Quality control
  • 5.3 Functions
  • 5.4 Utilities