Collection

📌 Some collections for GWAS and omics analyses ! ! !

✅ GWAS

🔧 This part collected various GWAS and post-GWAS tools

• GWAS tutorial: Genome-wide Association Studies (5cu) Matti Pirinen, University of Helsinki

• GWAS analysis:

  • BOLT-LMM
  • GCTA:
    • MLMA: mixed linear model based association analysis
    • fastGWA: A fast MLM-based Genome-Wide Association tool
    • fastGWA-GLMM: A fast GLMM(generalized linear mixed model)-based Genome-Wide Association tool
    • fastGWA-GE: A fast and powerful linear mixed model approach for genotype-environment interaction tests in large-scale GWAS
  • PLINK

• GWAS meta-analysis：

  • METAL
  • MTAG
  • PLINK

• Conditional and Joint analysis:

  • COJO: multi-SNP-based conditional & joint association analysis using GWAS summary data
  • meCOJO: multi-trait-based conditional & joint analysis using GWAS summary data

• Fine mapping:

  • GWFM
  • SuSiE
  • FINEMAP

• Integrate GAWS and Multi-omics:

  • SMR: an powerful approach of Jan Yang lab.
  • OPERA: an efficient and powerful approach to integrate omics data developed by Yang Wu
  • COLOC
  • MOLOC

• Genetic architecture:

  • SBayesS

• Mendelian Randomlisation:

  • GSMR
  • MR-Egger
  • TwoSampleMR

• Leveraging single cell & spatial with GWAS summary:

  • gsMap: integrates spatial transcriptomics (ST) data with GWAS for spatially resolved mapping of cells associated with human complex traits.
  • LDSC-SEG: cell type specific enrichment for SNP based heritability.
  • scDRS: a method for associating individual cells in single-cell RNA-seq data with disease GWASs

• Polygenic risk score:

  • SBayesRC: a method that incorporates functional genomic annotations with high-density SNPs (> 7 millions) for polygenic prediction.
  • LDpred2
  • PRScs:infers posterior SNP effect sizes under continuous shrinkage (CS) priors using GWAS summary statistics and an external LD reference panel.
  • PRScsx: integrates GWAS summary statistics and external LD reference panels from multiple populations to improve cross-population polygenic prediction.

✅ Omics

🔧 This part collected various multi omics tools

• QTL identification:
  • OSCA: a software tool for the analysis of complex traits using multi-omics data and genetic analysis of molecular phenotypes.
  • QTLtools: a tool set for molecular QTL discovery and analysis