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Table 2 Comparison of different features of well-known programs with EpiMINE

From: EpiMINE, a computational program for mining epigenomic data

User interface seqMINER HOMER ChIPseeqer Cistrome EpiMINE
GUI CL GUI WEB GUI GUI/CL
Standard analyses
 Peak calling FALSE TRUE TRUE TRUE FALSE
 Gene ontology FALSE FALSE TRUE FALSE FALSE
 Motif analysis FALSE TRUE TRUE TRUE FALSE
Peaks based analysis
 Enrichment of different samples in ROI FALSE FALSE FALSE FALSE TRUE
 Coexistence of different samples in ROI FALSE FALSE FALSE FALSE TRUE
 Correlation based on peaks FALSE FALSE TRUE FALSE FALSE
 Predicting dependencies based on peaks FALSE FALSE FALSE FALSE TRUE
 Introducing and analysing random regions FALSE FALSE FALSE FALSE TRUE
Quantification-based analysis
 Number of samples can be processed in a run 1 1 NA ≥1 (applicable for few cases) ≥1 (applicable for all cases)
 Works with raw data (no processing required) TRUE FALSE FALSE FALSE TRUE
 Signal within ROI FALSE FALSE FALSE FALSE TRUE
 Spread of Signal around ROI TRUE TRUE FALSE TRUE TRUE
 Profile generator TRUE TRUE FALSE TRUE TRUE
 Genome-wide/ROI-specific correlation FALSE FALSE FALSE TRUE TRUE
 Introducing and analysing random regions FALSE FALSE FALSE FALSE TRUE
 Provision of k-means clustering on quantified data TRUE Not in build FALSE TRUE TRUE
 Provision of hierarchical clustering on quantified data FALSE Not in build FALSE FALSE TRUE
 Correlating clustered data with expression FALSE FALSE FALSE FALSE TRUE
 Spike-in normalization FALSE FALSE FALSE FALSE TRUE
 Predicting dependencies based on peaks FALSE FALSE FALSE FALSE TRUE
 Filtering datasets on the basis of their importance wrt ROI FALSE FALSE FALSE FALSE TRUE
 Classification studies FALSE FALSE FALSE FALSE TRUE
User interface macs2 bdgdiff diffReps EpiMINE
CL CL GUI/CL
Differential studies
 Identifying differential regions between two conditions without replicates FALSE TRUE TRUE
 Identifying differential regions between two conditions with replicates TRUE TRUE TRUE
 Identifying differential regions between more than two conditions with replicates FALSE FALSE TRUE
  1. GUI graphical user interface, CL command line, TRUE feature is available in tool, FALSE feature is not available in tool, NA feature is not applicable for tool, Not in build feature should be executed outside the tool