methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data

BMC Bioinformatics

Table 1 Comparison of methylPipe and compEpiTools features with functionalities offered by other similar tools

		BiSeq	M3D	Bsseq	DSS	methylKit	methPipe	radMeth	methylSig	WBSA	DMAP	Methy-Pipe
methylPipe	Supporting targeted BS-seq data (e.g. RRBS)	+	+	+	+	+	+	+	+	+	+	+
	Supporting WGBS data	-	-	-	+	-	+	+	-	(a)	(b)	-
	Supporting multi-samples WGBS data	-	-	-	-	-	+	+	-	-	(b)	-
	Non-CpG mCs	-	-	-	-	-	-	-	-	+	-	+
	hmCs	-	-	-	-	+	+	-	-	-	-	-
	Supporting low-resolution DNA methylation data	-	-	-	-	-	-	-	-	-	-	-
	Computing absolute methylation (mC/bp)	-	-	-	-	-	-	-	-	-	-	-
	Computing relative methylation (mC/C)	+	-	+	-	+	+	-	+	+	-	+
	Supporting ROIs binning	-	-	-	-	-	-	-	-	-	-	-
	Pairwise DMR analysis (45’)	+ (NA)	+ (NA)	+ (NA)	+ (3d)	+ (NA)	+ (36’)	+ (90’)	+ (NA)	+ (a)	+	+ (NA)
	Multi-groups DMR analysis	-	-	+	-	-	-	+	-	-	+	-
	Browser-like data plot	-	-	-		-	-	-	+	-	-	-
compEpiTools	Computing Promoter-CpG content	-	-	-	-	-	-	-	-	-	-	-
	Routines for reads counting	-	-	-	-	-	-	-	-	-	-	-
	Determining Signal enrichment	-	-	-	-	-	-	-	-	-	-	-
	ROIs Annotation	+	-	-	-	+	-	-	+	+	+	-
	RNAPII stalling index	-	-	-	-	-	-	-	-	-	-	-
	Non-redundant GO enrichment enrichment	-	-	-	-	-	-	-	-	-	-	-
	Enhancers identification	-	-	-	-	-	-	-	-	-	-	-
	lncRNAs identification	-	-	-	-	-	-	-	-	-	-	-
	Integrative heatmaps	-	-	-	-	-	-	-	-	-	-	-
Ref.		[32]	[33]	[34]	[35]	[36]	[41]	[42]	[37]	[39]	[40]	[38]

The first column lists the key features offered by methylPipe and compEpiTools. Column headers report the tool name and reference. A “+” sign indicates that the feature is provided by a given tool, while a “–“sign indicates that it is not available. The “Pairwise DMR analysis” row includes in parenthesis the time (in minutes or days) needed for a complete WGBS differential analysis between two samples; NA is reported if this analysis is not supported for WGBS data. (a) WBSA is an online web-service imposing a limitation or 2GB for the upload of fastq files, which is clearly insufficient for the analysis of a WGBS dataset; the software can be installed locally although this requires significant effort (requiring Perl, R, MySQL, Java and C compiler) and it is only available for Linux; the analysis of the H1 and IMR90 WGBS was reported by the Authors to be completed in one week. (b) We could not use DMAP (no version details were provided for the code available) at the time of this comparison for the analysis of WGBS data, since an error was returned; a new version was provided to us, which was still requiring details on the restriction enzymes, necessary for the analysis of targeted DNA methylation datasets; eventually it remains unclear to us whether DMAP is able to analyse WGBS data

ISSN: 1471-2105