Software, Data, and Supplemental Files

Materials for McCoy et al., Cell. 2017

  • Code used for quantifying ASE
  • App to visualize ASE results
  • Multi-tissue ASE results for expressed tag SNPs
  • ExIBD: a software package for detecting Identity-by-descent (IBD) segments in exome sequencing data.

  • Compressed tar file containing ExIBD software package (236 MB)
  • Materials for Vernot et al. Science. 2016.

  • Directory of introgressed haplotype calls and frequencies
  • PhyloPNH: PhyloP scores calculated without the human reference genome from Fu et al. Am J Hum Genet. 2014.

  • Compressed tar file of PhyloPNH scores (GRCh37/hg19) (12 GB)
  • Materials for Vernot and Akey. Science. 2014.

  • Description of the files.
  • Compressed tar file of all introgressed regions
  • CCRARE: a java implementation of rare variant case/control association methods. O'Connor et al. PLOS One. 2013.

  • ccrare-0.1.jar
  • Zip of documentation, source, example, and jar files
  • Materials for Connelly et al. Genetics. 2012.

  • Zip of supplementary files (1.4 GB)
  • Materials for Skelly et al. Genome Research. 2011.

  • PDF tutorial describing how to use the code
  • R code for statistical model
  • Data from Akey et. al. PNAS. 2010.

  • Zip file of canine genotype data