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 |