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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