|
Armatus
|
C++ (C++11, boost) |
n × n interaction matrix -gzipped |
Calls TADs on raw and normalized matrices |
No |
Consensus of multi-resolution TAD analysis obtained from dynamic programming algorithm |
(37) https://github.com/kingsfordgroup/armatus/releases
|
|
Arrowhead
|
Java (none) |
hic format (Not from interaction matrix) |
Calls TADs-part of JuiceBox which has several other functionalities |
Yes |
Identification of domain corners using heuristics |
(14) http://www.aidenlab.org/commandlinetools/
|
|
DomainCaller
|
perl, matlab (none) |
n × (n+3) interaction matrix |
Calls TADs |
No |
Directionality index combined with hidden Markov model |
(12) http://chromosome.sdsc.edu/mouse/hi-c/download.html
|
|
HiCSeg
|
R, C |
n × n interaction matrix |
Calls TADs |
No |
Maximum likelihood segmentation using dynamic programming algorithm |
(38) https://cran.r-project.org/web/packages/HiCseg/index.html
|
|
TADbit
|
Python (Scipy, numpy, matplotlib, imp, mcl, chimera) |
n × n interaction matrix |
Mpas reads, normalizes and plots IF matrices. Calls and plots TADs. TAD clustering. 3D modelling |
No |
BIC-penalized breakpoint detection algorithm based on probabilistic interaction frequency model |
bioRxiv 036764 https://github.com/3DGenomes/tadbit/
|
|
TADtree
|
Python (Scipy, numpy) |
n × n interaction matrix |
Calls TADs |
Yes |
Hierarchical segmentation based on empirical distributions of interaction frequencies within TAD |
(43) http://compbio.cs.brown.edu/projects/tadtree/
|
|
TopDom
|
R |
n × (n + 3) interaction matrix |
Calls TADs |
No |
Heuristic for breakpoint detection combined with statistical filtering of false-positives |
(41) http://zhoulab.usc.edu/TopDom/
|
