title: MetaTopics: an integration tool to analyze microbial community profile by topic model.
abstract: Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between different bacteria in a microbial community keep unknown.
  
  
  
  MetaTopics can efficiently extract the latent microbial communities which reflect the intrinsic relations or interactions among several major microbes. Furthermore, a quantitative measurement, Quetelet Index, is defined to estimate the influence of a latent sub-community on a certain disease status for given samples. An analysis of our in-house oral metagenomics data and public gut microbe data was presented to demonstrate the application and usefulness of MetaTopics. To preset a user-friendly R package, we have built a dedicated website, https://github.com/bm2-lab/MetaTopics , which includes free downloads, detailed tutorials and illustration examples.
  
  
  
  MetaTopics is the first interactive R package to integrate the state-of-arts topic model derived from statistical learning community to analyze and visualize the metagenomics taxonomy data.
authors.affiliation: Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
authors.forename: Jifang
authors.initials: J
authors.lastname: Yan
authors.affiliation: Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
authors.forename: Guohui
authors.initials: G
authors.lastname: Chuai
authors.affiliation: Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Qi
authors.affiliation: Department of oral medicine, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School of Stomatology, Tongji University, Shanghai, China.
authors.forename: Fangyang
authors.initials: F
authors.lastname: Shao
authors.affiliation: Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
authors.forename: Chi
authors.initials: C
authors.lastname: Zhou
authors.affiliation: Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
authors.forename: Chenyu
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Yang
authors.affiliation: Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
authors.forename: Yifei
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Department of oral medicine, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School of Stomatology, Tongji University, Shanghai, China.
authors.forename: Cong
authors.initials: C
authors.lastname: Shi
authors.affiliation: School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Kang
authors.affiliation: Department of oral medicine, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School of Stomatology, Tongji University, Shanghai, China. drheyuan@tongji.edu.cn.
authors.forename: Yuan
authors.initials: Y
authors.lastname: He
authors.affiliation: Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China. qiliu@tongji.edu.cn.
authors.forename: Qi
authors.initials: Q
authors.lastname: Liu
mesh_terms: D019295:Computational Biology / Q000379:methods*; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota; D012984:Software; D064878:Web Browser
keywords: Disease status; Metagenomics; Microbial community; R; Topic model