CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

BMC Bioinformatics

Table 1 Features Provided by Programs that Identify Co-Expression Modules. Over representation analysis of CoP, and GeNET programs is considered “limited” because they only allow the usage of specific gene sets (GO, Pfam or KEGG). The runtime of 2 studies using the same computer and default settings are shown for CEMiTool, WGCNA, and Petal

Features	CEMiTool	WGCNA	Petal	CoP	GeNET	DiffCoEx	CoXpress	DICER	DINGO
Automatic Gene Filtering	yes	no	no	no	no	no	no	no	no
Over representation analysis	yes	yes	no	limited	limited	no	no	no	no
Gene set enrichment analysis	yes	no	no	no	yes	no	no	no	no
Integration with interactome	yes	no	no	no	no	no	no	no	no
Report in HTML	yes	no	no	yes	no	no	no	no	no
Native plots	yes	yes	no	no	yes	no	no	no	no
Search for a gene or gene list	yes	no	yes	yes	yes	no	no	no	no
Merging modules	yes	yes	no	no	no	yes	no	yes	no
Allows 2+ sample groups	yes	yes	yes	yes	yes	no	no	no	no
R package	yes	yes	yes	no	no	no	yes	no	yes
Year of last update	2017	2017	2017	2010	Unknown	Unknown	2013	Unknown	Unknown
Runtime for study GSE18090	2min12s	3min10s	17min18s	–	–	–	–	–	–
Runtime for study GSE43777	3min03s	4min33s	40min10s	–	–	–	–	–	–

ISSN: 1471-2105