一．数据标准化
1. HiCNorm
http://www.people.fas.harvard.edu/~junliu/HiCNorm/
2. ICE
https://mirnylab.bitbucket.io/hiclib/index.html
3. HiC-Pro
https://github.com/nservant/HiC-Pro
二. TAD鉴定
1.HiCseg:Models the uncertainty in Hi‐C data
https://cran.r-project.org/web/packages/HiCseg/index.html
2. TADbit
https://github.com/3DGenomes/TADbit
3.DomainCaller
http://chromosome.sdsc.edu/mouse/hi-c/download.html
4. InsulationScore:Robust to different sequencing depth;
can detect dynamics of TAD boundaries
https://github.com/dekkerlab/crane-nature-2015
5. Arrowhead:High computational efficiency with
dynamic programming
https://github.com/theaidenlab/juicer/wiki/Download
6. TADtree
文献：Identification of hierarchical chromatin domains
下载：TADtree
7. Armatus:TAD calling robust in different resolutions
https://github.com/kingsfordgroup/armatus
8. Topdom
http://zhoulab.usc.edu/TopDom/
9. HiCexplorer
HiCExplorer — HiCExplorer 3.3 documentation
三．交互片段鉴定（interaction）
1. Fit-Hi-C:Accurate background model using
non-parametric spline
http://noble.gs.washington.edu/proj/fit-hi-c
2. GOTHiC :Models contact-frequency uncertainty
as binomial distribution
http://bioconductor.org/packages/release/bioc/html/GOTHiC.html
3. HOMER
homer.ucsd.edu/homer/download.html
4. HIPPIE
wanglab.pcbi.upenn.edu/hippie
5. diffHic
https://bioconductor.org/packages/release/bioc/html/diffHic.html
6.HiCCUPS:Designed for high-resolution Hi‐C data
https://github.com/theaidenlab/juicer/wiki/Download
四．3D构象：
1. 3D-GNOME
https://bitbucket.org/3dome/3dome_mmc
2.Tadbit
https://github.com/3DGenomes/tadbit
五．可视化：
HiCPlotter
https://github.com/kcakdemir/HiCPlotter
以上内容搬运自：Hi-C三维基因组常用分析工具汇总
juicer同样具有诸多功能：juicer
还有一些其他的软件，可参考：ubuntu_19.10安装记录（二）
