We are developing algorithms and software tools for genomic data analysis.
Followings are the list of currently availabe software materials that we developred.
KEDDY is a statistical test method to identify gene sets with differential functional protein-protein interactions between given two conditions. KEDDY utilizes known functional protein-protein interaction information, and compares two conditions by evaluating the probability distributions of functional protein-protein interaction networks based on the known interactions. For gene sets with appropriate amount known protein-protein interactions, KEDDY provides advanced identification performance with reasonable computing requirement. A Java implementation of KEDDY is freely available to noncommercial users.
GVAF: A command line-based software for manipulating germline variants on annotated variant files
Germline Variant Annotation Filtering (GVAF) is designed to be used as aid tool in the process of efficient analysis of genomic variants by providing functionalities for exploring interest of variants form the result files consisting of arbitrary fields that contains abundant variant-related resources produced according to intended research direction. GVAF allows researchers to perform functionalities such as recognizing genotype-related fields from VCF files, adding additional annotations, filtering variants with a flexible and powerful filtering rules, and generating output files with customized formats. GVAF written in JAVA and bash script is freely available to non-commercial users.
Program commands and analysis scripts that were used for various analyses in the published articles from the lab.