OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data
作者机构：State Key Laboratory of Marine Environmental ScienceCollege of Ocean and Earth SciencesXiamen UniversityXiamen 361102FujianChina Hospital of StomatologyGuanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-Sen UniversityGuangzhou 510055GuangdongChina College of FisheriesGuangdong Ocean UniversityZhanjiang 524088GuangdongChina Fujian Institute for Sustainable OceansXiamen UniversityXiamen 361102FujianChina
出 版 物：《Horticulture Research》 (园艺研究（英文）)
年 卷 期：2023年第10卷第11期
页 面：13-26页
核心收录：
学科分类：0710[理学-生物学] 081203[工学-计算机应用技术] 08[工学] 0835[工学-软件工程] 0902[农学-园艺学] 0812[工学-计算机科学与技术（可授工学、理学学位）]
基 金：supported by grants from National Natural Science Foundation of China(32102775) Hainan Province Science and Technology Special Fund(ZDYF2022XDNY234) Earmarked Fund for CARS(No.CARS-49)and Fundamental Research Funds for the Central Universities(2072022)
主 题：breakthrough tables seeking
摘 要：With the advancements in high-throughput sequencing technologies such as Illumina,PacBio,and 10X Genomics platforms,and gas/liquid chromatography-mass spectrometry,large volumes of biological data in multiple formats can now be obtained through multi-omics *** is constantly evolving and seeking breakthroughs to solve multi-omics problems;however,it is challenging for most experimental biologists to analyse data using command-line interfaces,coding,and *** on experience with multi-omics,we have developed OmicsSuite,a desktop suite that comprehensively integrates statistics and multi-omics analysis and *** suite has 175 sub-applications in 12 categories,including Sequence,Statistics,Algorithm,Genomics,Transcriptomics,Enrichment,Proteomics,Metabolomics,Clinical,Microorganism,Single Cell,and Table *** created the user interface with Sequence View,Table View,and intelligent components based on JavaFX and the popular Shiny *** multi-omics analysis functions were developed based on BioJava and 300+packages provided by the R CRAN and Bioconductor communities,and it encompasses over 3000 adjustable parameter *** can directly read multi-omics raw data in FastA,FastQ,Mutation Annotation Format,mzML,Matrix,and HDF5 formats,and the programs emphasize data transfer directions and pipeline analysis *** can produce pre-publication images and tables,allowing users to focus on biological *** offersmulti-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in *** enables researchers to freely explore the molecular information contained in multi-omics big data(Source:https://***/OmicsSuite/,Website:https://***,v1.3.9).
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