Enrichment Analysis - Pathways and Networks

  • INRICH is a pathway analysis tool I developed for genome wide association studies (GWAS), designed for detecting enriched association signals of LD-independent genomic regions within biologically relevant gene sets.
  • MAGMA is another useful pathway analysis tool for GWAS that employs a principal component analysis-based regression framework. It is fast and features good power. 
  • ALIGATOR is a widely used pathway analysis tool developed for GWAS. With well-controlled type I error, it takes into account common genomic confounding factors. 
  • WGCNA is a gene-expression data analysis tool that can find clusters of highly correlated genes. It summarizes the identified clusters using module eigengenes or intramodular hub genes, and look for enriched biology or functions.
  • DAVID is one of the most widely used pathway analysis tool for high-throughput gene-based data (i.e., mRNA gene expression, proteomics data). It includes various functions, though be aware not to use this tool for genome data analysis!
  • DAPPLE looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature. 
  • DEPICT is an integrative GWAS analysis method that uses both established biological annotations and gene expression data. Given associated loci, It systematically prioritizes most likely causal genes by highlighting enriched pathways and relevant tissue/cell types.
  • ​CytoScape is a useful visualization tool for network and pathway findings. 

Genome-based Heritability Analysis

  • GCTA (Genome-wide Complex Trait Analysis) is by any means, the most widely used heritability analysis tool. It estimates the proportion of phenotypic variance explained by whole-genome genotype data. 
  • LDSC (LD SCore regression) is a heritability analysis tool that estimates SNP-heritability based on association summary statistics (no need for access to genotype data). 
  • LDAK (Linkage Disequilibrium Adjusted Kinships) is a heritability analysis tool that creates kinship matrices adjusted for LD between genotype markers.  
  • MEGHA (Massively Expedited Genome-wide Heritability Analysis) is a matlab toolbox and R package for fast heritability analysis of high dimensional phenotype data, such as neuroimaging traits. 
  • LDRegress is Implemented in the EIGENSOFT software, LDregress is a heritability analysis tool that adjusts LD between genotype markers using regression.  
  • PCGC (Phenotype Correlation-Genotype Correlation) is a regression-based method for heritability estimation. 

Genome-Wide Association Analysis (GWAS)

  • PLINK is the most comprehensive software package for GWAS. 
  • EIGENSOFT is a useful software package, specially for adjusting population stratification.  
  • Minimac is a fast imputation tool with a detailed protocol with 1000 genome data.
  • BEAGLE is another Another imputation package for phasing and inferring missing genotype data.  
  • METAL is a widely used meta analysis tool for whole genome data analysis. 
  • LocusZoom is a good plotting tool for regional GWAS association results. 
  • MQFAM is a multivariate association analysis tool that uses canonical correlation. 

Rare Variant Data Analysis

  • zCall is a calling algorithm designed for array-based genotyping data of rare variants.
  • PLINK/SEQ is an open-source C/C++ library designed for large-scale sequencing data analysis. 
  • The VEP (Variant Effect Predictor) determines the functional effect of variants, including SNPs, insertions, deletions, CNVs or structural variants on genes, transcripts, and protein sequence, as well as regulatory regions. 
  • RV-Test is a stand-alone rare variant testing package that can analyze both population-based and related samples.

Gene Expression and Regulatory Data Resources

  • The BrainSpan Atlas is a foundational resource for studying transcriptional mechanisms involved in human brain development.
  • The BrainCloud is a stand-alone GUI tool for exploring the temporal dynamics and genetic control of transcription in the human prefrontal cortex across the lifespan. 
  • The PsychENCODE project aims to generate a public resource of genomic, regulatory, epigenomic, transcriptomic, and proteomic data in healthy and diseased developing and adult human brains.

Neuroimaging Genomics Resources

  • The ENIGMA Consortium is the largest international efforts in neuroimaging genomics to study brain structure, function and disease. 
  • BRAINnet is an innovative research initiative that shares a collection of neuroimaging, cognitive, clinical, and genomic data for accelerating brain research.