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Workflow systems and pipelines are essential in computational biology and bioinformatics due to the complexity of the analyses and the diversity of tools and libraries that must be used. This is true for RNA-Seq differential expression analyses, where selecting a pipeline (i.e. steps and specific tools) depends on the study’s specific needs, including reproducibility, user-friendliness, and the capacity to process complex genomes and experimental designs. Differential expression analysis tools include the well-known edgeR, limma, DESeq2, and dearseq libraries, among others, which are available as part of other libraries like DElite, which also offers a statistically combined output of such four tools, as well as of other pipelines like VIPER, RNAflow, or DEWE, developed by our group a few years ago. This work presents a conversion of the DEWE graphical user interface tool into a 100% command-line Compi pipeline. This updated version includes featureCounts as an alternative to HTSeq for counting reads and also relies on DElite for performing the differential expression analysis.

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A New Compi Pipeline for RNA-Seq Differential Expression Analysis

  • 会议论文

  • 发表日期：

    2026年

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  • Rosalinda Di Gerlando,
  • Stella Gagliardi,
  • Hugo López-Fernández

摘要

Workflow systems and pipelines are essential in computational biology and bioinformatics due to the complexity of the analyses and the diversity of tools and libraries that must be used. This is true for RNA-Seq differential expression analyses, where selecting a pipeline (i.e. steps and specific tools) depends on the study’s specific needs, including reproducibility, user-friendliness, and the capacity to process complex genomes and experimental designs. Differential expression analysis tools include the well-known edgeR, limma, DESeq2, and dearseq libraries, among others, which are available as part of other libraries like DElite, which also offers a statistically combined output of such four tools, as well as of other pipelines like VIPER, RNAflow, or DEWE, developed by our group a few years ago. This work presents a conversion of the DEWE graphical user interface tool into a 100% command-line Compi pipeline. This updated version includes featureCounts as an alternative to HTSeq for counting reads and also relies on DElite for performing the differential expression analysis.