Fig. 1
From: methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data
Diagram describing input and output for the methylPipe and compEpiTools R packages. Most typical input data and output are listed for both packages. Regions of interest (ROIs) might be both input and output for these tools. For example, input ROIs can be generated in R based on the UCSC table browser or can be based on Bioconductor gene models or reference genome-sequence packages. Output ROIs are generated by methylPipe and compEpiTools and can typically feedback on the same tools as a new set of genomic regions to be investigated, often associated with scores or more complex data. Abbreviations: differentially methylated regions (DMRs); methyl-cytosine (mC); CpG Islands (CGIs); GeneOntology (GO); long non-coding RNAs (lncRNAs); transcription factors (TFs). The dashed arrow identifies a computational step that can be covered with additional tools (see the text for details)