| Functions | Applications | Input files | Main output files | Programs | References |
| Co-expression and Gene Ontology Enrichment Analysis | Invesitgate the putative function of assembled transcripts through co-expression network and GO enrichment analysis | Invesitgate the putative function of assembled transcripts through co-expression network and GO enrichment analysis | Co-expression result tables; Diagnostic plot (Dendrogram); GO analysis table | WGCNA (version 1.63; https://cran.r-project.org/web/packages/WGCNA/index.html) | Langfelder P et al., 2008 |
| topGO (version 3.7; https://bioconductor.org/packages/release/bioc/html/topGO.html) | Alexa A et al., 2010 |