HiC分析工具汇总

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）