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EcoOmicsAnalyst employs the following software packages:

  • Fastp for raw reads quality check
  • Kallisto for gene quantification (with reference transcriptome);
  • Tximport for tidy gene abundance table;
  • Seq2Fun for raw reads processing and gene quantification (without reference transcriptome);

To supplement EcoOmicsAnalyst we provide ExpressAnalyst for downstream statistical analysis and EcoOmicsDB for viewing ortholog evidence. A typical workflow with the three tools is below:

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