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The Zachary Kaminsky Lab Software
We present a free open-source Perl application, Binding Intensity Only Tile array analysis or “BioTile”, for the identification of differentially enriched regions (DERs) in tiling array data. BioTile exhibits higher power to identify significant DMRs of low effect size and across shorter genomic stretches as compared to other ‘peak’ finding algorithms. BioTile represents an easy to use analysis option applicable to multiple microarray platforms, allowing for its integration into the analysis workflow of any project. The BioTile Perl script is available for download here and is compatible with Linux, Mac-OS, and MS-Windows operating systems. It requires the installation of Perl, which is freely available at the Comprehensive Perl Archive Network (CPAN) at (www.cpan.org).
Documentation | For detailed instructions on how to use BioTile, click here.
Package Downloads | BioTile BioTile.zip | In press at BMC Bioinformatics
Citation | In press at BMC Bioinformatics
We present a free open-source R package, Cell EpigenoType Specific (CETS) mapper, designed for the quantification and normalization of differing neuronal proportions in genome-scale DNA methylation datasets. The application of CETS quantification and transformation can reduce heterogeneity and improve replicability of epigenetic findings in the brain across cohorts. The CETS package is available for download here and is compatible with Linux, Mac-OS, and MS-Windows operating systems. It requires the installation of R, which is freely available at the Comprehensive R Archive Network (CRAN) at (cran.r-project.org).
Documentation | For detailed instructions on how to use CETS, click here.