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GenGen: Genetic Genomics Analysis of Complex Data

eagle-i ID


Resource Type

  1. Algorithmic software suite


  1. Resource Description
    "GenGen is a suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated. Some of the most useful and more stable programs in this package are: • calculate_association.pl: perform genome-wide association analysis for cohorts with case-control design and trio design, with ability to handle PLINK-formatted TPED/TFAM files and handle phenotype permutations. • calculate_gsea.pl, combine_gsea.pl: use pathway-based approaches to test the significane of genes within a pathway for genome-wide association studies (see reference below). • scan_region.pl: scan two sets of genomic regions to find overlap (for example, scan most conserved genomic elements, scan transcription factor binding sites, scan segmental duplication regions, scan predicted microRNA sites, scan pseudogenes, scan EvoFold regions, etc. • convert_mach.pl, convert_mach2snptest.pl, combine_snptest.pl: convert MACH-imputed genotype data sets into standard PED/MAP format or SNPTEST format for subsequent association test. • convert_bim_allele.pl: convert SNP allele coding between Illumina A/B alleles, Illumina 1/2 alleles, Illumina TOP strand alleles and dbSNP forward strand alleles. • retrieve_ensembl.pl, retrieve_variation.pl, retrieve_compara.pl: query the Ensembl databases to get the desired information on genes, transcripts, variations, cross-references, domains, predicted regulatory elements and so on."
  2. Used by
    Bucan Laboratory
  3. Operating System
  4. Operating System
  5. Operating System
  6. Related Publication or Documentation
    Pathway-Based Approaches for Analysis of Genomewide Association Studies
  7. Related Publication or Documentation
    Common genetic variants on 5p14.1 associate with autism spectrum disorders
  8. Website(s)
  9. Related Technique
    Single-nucleotide polymorphism analysis
  10. Related Technique
    Bioinformatics analysis
  11. Coded in
  12. Coded in
Provenance Metadata About This Resource Record
  1. workflow state
  2. contributor
    ggrant (Gregory Grant)
  3. created
  4. creator
  5. modified
Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016