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Table 1 Searchlight features and comparison with VIPER and Biojupies

From: Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts

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, 1 GB RAM 1 core, 1 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