Table 1 Feature Comparison
Feature | CisGenome [44] | unix tool scripting [45] | Fish the Chips [46] | R pipeline [47] | HiChIP [48] | Cistrome [49] | This package |
|---|---|---|---|---|---|---|---|
Primary implementation | C | unix tools | C++ | C and R | R | Galaxy | R and Kepler |
Single modules available | no | noa | no | no | no | yes | yes |
Single turnkey pipeline | no | no | yes | no | yes | no | yes |
Interface | GUI, command line | command line | GUI, command line | command line | command line | web | GUI (Kepler) + command line |
Data provenance tracking | no | no | no | no | no | yes (Galaxy) | yes (Kepler) |
Generate genome browser track | yes (custom) | yes (UCSC) | yes (UCSC) | no | yes (UCSC) | yes (UCSC) | yes (UCSC) |
Peak calling | yes (custom) | yes (MACS) | yes (MACS) | yes (PICS) | yes (MACS and SICER) | yes (MACS) | yes (MACS) |
Summary peak statistics | yes | yes | yes | no | yes | yes | yes |
Summary location statistics | yes | yes | yes | no | yes | yes | yes |
Map to nearby genes | yes | yes | yes | no | yes | yes | yes |
Automatic generation of peak graphs | no | no | no | no | no | no | yes |
Heatmap of read density | no | no | no | no | yes | yes | yes |
Average profiles | no | no | no | no | yes | yes | yes |
De novo motif analysis | yes | yes (MEME) | no | yes (rGADEM) | yes (MEME) | yes (SeqPos) | yes (MEME) |
Motif enrichment analysis | yes | yes | no | yes | no | yes | no |
Gene ontology | no | yes | no | no | yes(custom) | nob | yes |
Pathway analysis | no | no | no | no | no | no | yes |