Table 2.
Examples of interoperability of the Nextcast data formats with external tools.
| Nextcast Component | Output | External tool | Description | |
|---|---|---|---|---|
| eUTOPIA | gene expression matrix | MORPHEUS | https://software.broadinstitute.org/morpheus | |
| eUTOPIA | gene expression matrix | t-SNE [82], UMAP [83] | Dimensionality reduction techniques available in R or Python | |
| eUTOPIA | differentially expressed genes | WebGestalt [84], Enrichr [85], PathwAX [86], Ingenuity Pathway Analysis (QIAGEN Inc.,https://digitalinsights.qiagen.com/IPA) | Pathway enrichment analysis | |
| eUTOPIA | differentially expressed genes | STRING [87] | https://string-db.org/ | |
| FunMappOne | enriched GO terms | REVIGO | Tool for summarization and to study of GO terms interactions (available athttp://revigo.irb.hr/) | |
| INfORM | Co-expression networks | Cytoscape [88] and Gephy [89] G | Tools for network visualisation | |
| INfORM | Prioritised genes | WebGestalt [84], Enrichr [85], PathwAX [86], Ingenuity Pathway Analysis (QIAGEN Inc.,https://digitalinsights.qiagen.com/IPA) | Pathway enrichment analysis | |
| INfORM | Prioritised genes | STRING [87] | https://string-db.org/ |