OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data

作者：Ben‐Ben Miao, Wei Dong, Yixin Gu, Zhaofang Han, Xuan Luo, Caihuan Ke, Weiwei You · 发表于：Horticulture Research · 年份：2023 · DOI：10.1093/hr/uhad195 · 被引用次数：30 · 研究领域：Bioinformatics and Genomic Networks、Gene expression and cancer classification、Genetic Mapping and Diversity in Plants and Animals

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 analysis. Bioinformatics 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 scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The 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 interfaces. OmicsSuite 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 functions. OmicsSuite can produce pre-publication images and tables, allow...