Development And Application Of Multi-omics Interactive Analysis Tools Based On R/Shiny

With the rapid development of the second-generation sequencing technology,genome and transcriptome sequencing have become the most commonly used tools for exploring the genome and transcriptome of organisms in life science research.During the rapid development of the second-generation sequencing technology,a big amount of transcriptome and genome sequencing data have been generated.However,due to the popularization of bioinformatics lags far behind the generation rate of sequencing data,most researchers in the life science are unable to analyze the existing sequencing data.Although there are currently many analysis software available for sequencing data analysis,most of them requires a certain level of computer knowledge.Compared with command-line code,the interactive analysis page for data upload,analysis,and visualization is more acceptable to researchers.In this study,we designed and constructed two R packages based on R language,named VCFshiny and QRAP,which can quickly and easily analyze and visualize genome and transcriptome sequencing data.1.VCFshiny can effectively extract mutation information of the genome and perform detailed analysis,including detecting sample duplication quality,summarizing the number of variations in each sample,analyzing single nucleotide variation types,detecting the length distribution of insertions and deletions,depicting the distribution of variations on the genome,and screening sample for high frequency mutation genes.2.QRAP can easily perform RNA-seq data analysis and visualization through a user-friendly web interface.As a comprehensive RNA-seq analysis tool,QRAP can support the analysis of public data and user-generated data,including routine RNA-seq data,time-course RNA-seq data,and clinically relevant RNA-seq data,and provide functional annotations for about 500 species.In each analysis step,we provide multiple visualization methods to help users obtain high-quality images that can be directly used for publication or sharing.Overall,we have successfully constructed two interactive analysis tools based on R/Shiny,which can perform interactive analysis and visualization of genome and transcriptome sequencing data.The two tools are characterized by simple operation,fast analysis,comprehensive functions,and do not require programming foundation.They can quickly and easily complete the data analysis of genome and transcriptome sequencing,reducing the learning cost and time cost of researchers in sequencing data analysis.