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methylPipe and compEpiTools: a suite of R packages for the integrative analysis
of epigenomics data
#MMPMID26415965
Kishore K
; de Pretis S
; Lister R
; Morelli MJ
; Bianchi V
; Amati B
; Ecker JR
; Pelizzola M
BMC Bioinformatics
2015[Sep]; 16
(?): 313
PMID26415965
show ga
BACKGROUND: Numerous methods are available to profile several epigenetic marks,
providing data with different genome coverage and resolution. Large epigenomic
datasets are then generated, and often combined with other high-throughput data,
including RNA-seq, ChIP-seq for transcription factors (TFs) binding and DNase-seq
experiments. Despite the numerous computational tools covering specific steps in
the analysis of large-scale epigenomics data, comprehensive software solutions
for their integrative analysis are still missing. Multiple tools must be
identified and combined to jointly analyze histone marks, TFs binding and other
-omics data together with DNA methylation data, complicating the analysis of
these data and their integration with publicly available datasets. RESULTS: To
overcome the burden of integrating various data types with multiple tools, we
developed two companion R/Bioconductor packages. The former, methylPipe, is
tailored to the analysis of high- or low-resolution DNA methylomes in several
species, accommodating (hydroxy-)methyl-cytosines in both CpG and non-CpG
sequence context. The analysis of multiple whole-genome bisulfite sequencing
experiments is supported, while maintaining the ability of integrating targeted
genomic data. The latter, compEpiTools, seamlessly incorporates the results
obtained with methylPipe and supports their integration with other epigenomics
data. It provides a number of methods to score these data in regions of interest,
leading to the identification of enhancers, lncRNAs, and RNAPII
stalling/elongation dynamics. Moreover, it allows a fast and comprehensive
annotation of the resulting genomic regions, and the association of the
corresponding genes with non-redundant GeneOntology terms. Finally, the package
includes a flexible method based on heatmaps for the integration of various data
types, combining annotation tracks with continuous or categorical data tracks.
CONCLUSIONS: methylPipe and compEpiTools provide a comprehensive
Bioconductor-compliant solution for the integrative analysis of heterogeneous
epigenomics data. These packages are instrumental in providing biologists with
minimal R skills a complete toolkit facilitating the analysis of their own data,
or in accelerating the analyses performed by more experienced bioinformaticians.
free
free
free
