UNC Computational Genetics

NPUTE

NPUTE software package - A fast algorithm for imputing missing genotypes in SNPs, currently under development

snpBrowser

Executable

• [Download] snpBrowser v0.6, Windows executable (includes the SNP files for the 74-strain dataset and the .GENE gene annotations)
  • Un-zip the file and run “view.exe”. .GENE & .SNP files are located in the “Gene Files” and “SNP Files” folders respectively

Source Code

• [Download] snpBrowser v0.6, Python source code
  • Required packages: NumPy, PIL, wx
  • Latest builds can be found in the CompGen SVN repository
• [Download] Example .SNP/.POS/.MSK file generator, Python source code. Example raw CSV SNP file included (source).

Datasets

• Perlegen: 16 strains, 8.3 million SNPs, majority imputed (source)
  • [Download] .SNP files
  • [Download] .POS files - not required for functioning of application
• Imputed 74-strain: 74 strains, 7.8 million SNPs, HMM imputed (source)
  • [Download] .SNP files (packaged with application)
  • [Download] .POS files - not required for functioning of application
  • [Download] .MSK files - not required for functioning of application
• Gene annotations (source) - packaged with application
  • [Download] .GENE files (packaged with application)

Documentation

• [Download] User’s Manual/Design & Implementation Documentation - a thorough guide to the various functions of the application; includes pertinent design & implementation documentation
• [Go] PyDoc-generated Module Definitions (HTML)
• [Download] Example CSV phenotype file (source). Phenotype file can be loaded in, instead of manually typing in each value into the application. Example is for the imputed 74-strain set.

Miscellaneous

• [Download] 5-minute PowerPoint presentation on snpBrowser; 12-6-07 UNC-CH Computational Genetics Meeting
• [Download] 30-minute PowerPoint presentation on snpBrowser;4-25-08 UNC-CH CS Undergraduate Honors Presentation