GenGen main package

The stable version of GenGen main package can be downloaded below. The main package DOES NOT include the necessary library files.

GitHub Repository

Supplementary library files

SNP-gene mapping files for various Illumina and Affymetrix SNP arrays, as well as SNPTable file for commonly used arrays, can be downloaded below.


Among the SNP-gene mapping files, hh550* are for HumanHap550 array, hhall* are for other Illumina Infinium arrays, affy500k* are for Affymetrix 500K arrays, gw6* are for Affymetrix genome-wide 6.0 arrays. You can contact me directly to get SNP-gene mapping annotation for other arrays. Or, you can follow the instructions to generate a custom annotation file using the program included in the package. Among the SNPTable files, hh550_610.snptable is for Illumina 550K or 610K arrays (all versions), and hh1mv13.snptable is for Illumina 1M arrays (version 1 or 3).

SNPTable file for Illumina arrays and Affymetrix arrays

Contact me with issues/bugs in these files as they were not tested by me.

You can generate a SNPTable file yourself by downloading the manifest file from Illumina. This is a comma-delimited CSV file and you only need to extract the four relevant columns from this file, then save as tab-delimited formats.