Burçak Otlu1, Can Firtina2, Sündüz Keles3, Oznur Tastan2. 1. Department of Computer Engineering, Middle East Technical University, 06800, Ankara, Turkey. 2. Department of Computer Engineering, Bilkent University, 06800, Ankara, Turkey. 3. Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA.
Abstract
MOTIVATION: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. RESULTS: We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis. AVAILABILITY AND IMPLEMENTATION: GLANET can be run using its GUI or on command line. GLANET's source code is available at https://github.com/burcakotlu/GLANET . Tutorials are provided at https://glanet.readthedocs.org . CONTACT: burcak@ceng.metu.edu.tr or oznur.tastan@cs.bilkent.edu.tr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. RESULTS: We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis. AVAILABILITY AND IMPLEMENTATION: GLANET can be run using its GUI or on command line. GLANET's source code is available at https://github.com/burcakotlu/GLANET . Tutorials are provided at https://glanet.readthedocs.org . CONTACT: burcak@ceng.metu.edu.tr or oznur.tastan@cs.bilkent.edu.tr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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