| FAN-C | Cooler3 | Juicer | HOMER | HiC-Pro | HiC-bench | TADbit | HiFive | HicDat | HiC-inspector | HiCUP | HiCExplorer | HiCeekR |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
User interfaces | |||||||||||||
 Command line | x | x | x | x | x | x | x | x |  | x | x | x |  |
 Programmatic access (API) | x | x | x |  |  |  | x | x | x |  |  |  |  |
 Graphical user interface (GUI) | 1 | 1 | 4 |  |  |  | 1 |  | 11 | 12 |  | 18 | x |
Supported formats | |||||||||||||
 Directly compatible | |||||||||||||
 Juicer | x |  | x |  |  | 20 |  |  |  |  |  |  |  |
 Cooler | x | x |  |  |  | 20 |  |  |  |  |  | x |  |
 Custom/Native | x | x | x | x | x | x | x | x | x | x | x | x | x |
 Import | |||||||||||||
 Juicer | x | x |  |  | x |  |  |  |  |  |  | x |  |
 Cooler | x | x |  |  | x |  | x |  |  |  |  | x |  |
 TXT file | x | x |  | x | x | x | x | x |  | x |  | x |  |
 FASTQ | x | x | x | 5 | x | x | x |  | 5 | x | x | x |  |
 SAM/BAM | x | x | x | x | x | x | x | x | x |  |  | x |  |
 hiclib |  | x |  |  |  |  |  |  |  |  |  |  |  |
 Export | |||||||||||||
 Juicer | x |  | x | x | x | 20 |  |  |  |  | x |  |  |
 Cooler | x | x |  |  | x | 20 | x |  |  |  |  | x |  |
 GInteractions |  |  |  |  |  |  |  |  |  |  |  | x |  |
 TXT file | x | x | x | x | x | x | x |  |  | x | x | x | x |
Matrix generation | |||||||||||||
 FASTQ mapping | |||||||||||||
 Simple mapping | x | x |  | 5 | x | x | x |  | 5 | x | x | 5 |  |
 Iterative mapping | x |  |  |  |  |  | x |  |  |  |  |  |  |
 Ligation junction split | x |  | x | x | x |  | x |  |  |  | x |  |  |
 Read/region pair filtering | |||||||||||||
 Mapping Quality | x | x | x |  | x | x |  |  |  |  | x | x |  |
 Multi-mapping reads | x | x | x |  | x | x | x |  |  |  | x | x |  |
 Restriction site distance | x | x | x | x |  | x | x | x |  | x | x | x | x |
 Ligation errors | x | x | x |  | x |  | x | x | x |  | x | x | x |
 Self-ligations | x | x | x | x | x | x | x | x | x |  | x | x | x |
 PCR duplicates | x | x | x | x | x | x | x | x |  |  | x | x | 15 |
 Unusual read density |  | x |  | x |  |  | x |  |  |  |  |  |  |
 Quality statistics | x | x | x | x | x | x | x | x |  | x | x | x |  |
 Hi-C processing | |||||||||||||
 Fragment-level Hi-C | x | x | x | x | x | x |  | x | x |  |  | x |  |
 Equi-distant bins | x | x | x | x | x | x | x | x | x | x |  | x | x |
 Multi-resolution Hi-C | 2 | x | x |  |  | 20 |  | x |  |  |  | x |  |
 Matrix balancing | x | x | x | x | x | x | x | x | x |  |  | x | x |
 Probabilistic normalisation |  |  |  |  |  |  |  | x | x |  |  |  |  |
 Matrix merge | x | x | x |  |  | x | x |  | x |  |  | x |  |
 Allele-specific matrices |  | x | x |  | x |  |  |  |  |  |  |  |  |
 Mixed restriction cut sites | x | x | x |  | x |  |  |  |  |  |  | x |  |
 Hi-C filtering | |||||||||||||
 Minimum coverage | x | x |  |  | x |  | x | x |  |  |  |  |  |
 Diagonal | x | x |  |  | x | x |  |  |  |  |  |  |  |
Matrix analysis | |||||||||||||
 Comparisons | |||||||||||||
 PCA (sample comparison) | x | 17 |  |  |  | 21 |  |  |  |  |  |  |  |
 Matrix fold-change | x | x | x |  |  | 20 |  |  | x |  |  | x |  |
 Matrix difference | x | 17 | x |  |  | 20 |  |  |  |  |  | x |  |
 Score/feature comparisons | x | 17 | x | x |  | x | x |  |  |  |  | x |  |
 Correlations |  | 17 | x | x |  | x | x |  | x |  |  | x |  |
 Domains | |||||||||||||
 Insulation score | x | x |  |  |  | x | x |  |  |  |  | x |  |
 Directionality index | x | x |  |  |  | x |  |  |  |  |  |  | x |
 Arrowhead |  |  | x |  |  |  |  |  |  |  |  |  |  |
 TAD calling |  |  | x | x |  | x | x |  |  |  |  | 19 | x |
 Loops | |||||||||||||
 HICCUPS | x | x | x |  |  |  |  |  |  |  |  |  |  |
 Other |  |  |  | x | 7 | 10 |  |  |  |  |  | x |  |
 Common Hi-C analyses | |||||||||||||
 Expected values | x | x | x | x |  | x | x | x | x | x |  | x |  |
 AB compartments | x | x | x | x |  | 20 | x |  | x |  |  | x | x |
 Aggregate Hi-C matrices | x | x | x |  |  |  |  |  |  |  |  | x |  |
 3D modelling |  |  | 16 |  |  |  | x |  |  |  |  |  |  |
 Other | |||||||||||||
 Compaction |  |  |  | x |  |  |  |  |  |  |  |  |  |
Visualisation | |||||||||||||
 Hi-C matrix | x | x | x | 6 | 8 | 8 | 22 | x | x | x | 13 | x | x |
 Triangular Hi-C matrix | x | x |  | 6 | 8 | 8 | 22 | x |  |  |  | x |  |
 Other genomic tracks | x | x | x |  | 8 | 8 | 22 |  |  |  |  | 14 | x |
 Genes | x | x | x |  | 8 | 8 | 22 |  |  |  |  |  |  |
 Virtual 4C | x | x | x |  |  | 8 |  |  |  |  |  |  |  |