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Table 1 Comparison with existing visualization and analysis software. Comparison of ChARMView's functionality with existing visualization and analysis software including Caryoscope [11], CGHAnalyzer [12], Java Treeview's Karyoscope [13], SeeCGH [14], CGH-Explorer [24], CGH-PRO [25], and CGH-Miner [26].

From: Visualization-based discovery and analysis of genomic aberrations in microarray data

Feature

ChARM View

Caryo-scope

TreeView (Karyosco pe)

SeeGH

CGH Analyzer

CGH Explorer

CGH PRO

CGH Miner

Platform

most platforms (Java-based)

most platforms (Java-based)

most platforms (Java-based)

Windows

most platforms (Java-based)

most platforms (Java-based)

Linux, Windows

Windows, Unix, Excel add-in

Software availability

freely downloadab le with registration

freely downloadable

freely downloadable

freely downloadab le with registration

freely downloadable with registration

freely downloadable with registration

freely downloadab le

freely downloadable with registration

Source-code license

GNU GPL

MIT license

GNU GPL

not available

freely downloadable

freely downloadable

GNU GPL

freely downloadable

External software dependencies

none

none

none

requires MySQL database

none

none

MySQL, R

R

Automatic statistical determination of single-array aberrations

Yes

No

No

No

No

Yes

Yes

Yes

Statistical analysis of manually selected regions

Yes

No

No

No

Yes

Yes

No

No

Simultaneous display of multiple experiments

Yes

No

No

No

Yes

Yes

Yes

Yes

Statistical analysis of aberrations occurring in multiple experiments

No

No

No

No

Yes

No

No

No

Aberration breakpoints/statistics export

Yes

No

No

No

Yes

Yes

Yes

Yes

Image export

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Command-line statistical analysis feature

Yes

No

No

No

No

No

No

No

Allows user-defined genomic feature annotation

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Web-linked genomic feature annotation

No

Yes

Yes

Yes

Yes

Yes

Yes

No