BSXplorer: analytical framework for exploratory analysis of BS-seq data

BMC Bioinformatics

Table 1 Overview of BSXplorer features and comparison with other tools

	BSXplorer	MethGET	ViewBS	RnBeads	msPIPE	MethylC-analyzer
All-in-one
BS-seq data analysis solution	No	No	No	Yes	Yes	Yes
CLI	Yes	Yes	Yes	Yes	No	No
API	Yes	No	No	Yes	No	No
Array support	No	No	No	Yes	No	No
Methylation data input format	Bismark (bedGraph, cov, CX_report), BS-Seeker2	BS-Seeker2, Bismark, BSMAP, methylpy, METHimpute	Bismark (CX_report), BSSeeker, BRAT	Array data, BS-seq fastq	BS-seq fastq	BS-Seeker, Bismark, BSMAP, METHImpute
Metagene line/heatmap plots	Yes	Metagene only	Yes	Yes	No	Yes
Genome annotation format	BED, GFF/GTF, custom	GTF	BED	Inbuilt set of human, mouse, rat genome annotations	Online access to USCS genomes	GTF
Regions-of-interest support	Yes	No	Yes	Yes	No	No
Intraspecies comparison	Yes	No	Yes	No	No	No
Data export for downstream analysis	Yes	No	Yes (RDS format)	No	Yes	Yes
Chromosome-level methylation	Yes	No	Yes	Yes	Yes	Yes
Comparative analysis of methylation profiles in different types of genomic elements	Yes	No	Yes	Yes	No	No
Comparative analysis of methylation profiles between experimental samples	Yes	Yes	Yes	Yes	No	Yes
Clustering of methylation profiles within the same experimental sample	Yes	No	No	No	No	No
Hypertext report generation	Yes	No	No	Yes	No	No
Non-model organism analysis support	Yes	Yes	Yes	No	Only USCS genomes	Yes
Genic DNA methylation pattern classification (i.e., Takuno & Gaut P_CG statistics)	Yes	No	No	No	No	No

ISSN: 1471-2105