Feature | Searchlight | Viper | BioJupies |
---|---|---|---|
Source code available | Yes | Yes | Yes |
Type of tool | Command line | Command line | Web |
Operating system | Linux/Unix/Windows | Linux/Unix | Any |
Computing resources needed (EVI) | 1 core, 1Â GB RAM | 1 core, 1Â GB RAM | None |
Easy to set up and run | Yes | Yes | Yes—very |
Graphical user interface for pipeline | No | No | Yes |
Level of automation | Full | Full | Partial |
Organism | Any | Any | Human and mouse |
Processing pipeline | No | Yes | Yes |
EVI pipeline | Yes | Yes | Yes |
Intermediate files | Yes | Yes | Yes |
Support for complex experimental designs (i.e. more than two different groups of samples) | Yes | Partial | None |
Pathway analysis | Over-representation, upstream regulator, differential expression signatures | Over-representation, gene-set enrichment, gene interaction | Over-representation |
Total visualisation types (n) | 50 | 20 | 12 |
Quality control visualisation types (n) | 1 | 5 | 1 |
Expression visualisation types (n) | 7 | 6 | 2 |
Differential expression visualisation types (n) | 33 | 5 | 9 |
Multiple differential expression visualisation types (n) | 9 | 1 | 0 |
Other visualisation types (n) | 0 | 3 | 0 |
Plots visually consistent | Yes | No | Yes |
Support for downstream user modification of plots | Yes | No | Partial |
Graphical user interface for plot modification | Yes | No | Yes |
Produces a report | Yes | Yes | Yes |
Full report (i.e. descriptions, legends and methods) | Yes | No | Yes |