COSINE: A Web Server for Clonal and Subclonal Structure Inferencing and Evolution in Cancer Genomics，clab-cosine.net, http://www.clab-cosine.net/ or http://bio.rj.run:48996/cun-web/ . Here are manuscript of COSINE:
Xiguo Yuan, Yuan Zhao, Yang Guo, Linmei Ge, Wei Liu, Shiyu Wen, Qi Li, Zhangbo Wan, Peina Zheng, Tao Guo, Zhida Li, Martin Peifer, Yupeng Cun, COSINE: A Web Server for Clonal and Subclonal Structure Inference and Evolution in Cancer Genomics, 2021, preprint at arXiv.
COSINE contain these methods:
- 1. Sclust: Software: http://rj.run/downloads/Sclust.tgz
- 2. Pyclone: Software: https://shahlab.ca/projects/pyclone/
- 3. FastClone: Software: https://github.com/GuanLab/FastClone_Guanlab
- 4. Dpclust: Software: https://github.com/Wedge-Oxford/dpclust
- 5. phyloWGs: Software: https://github.com/morrislab/phylowgs
- 6. SciClone: Software: https://github.com/genome/sciclone
- 7. Svclone: Software: https://github.com/mcmero/Svclone
- 8. CLiP: Software: https://github.com/wwylab/CliP
- 9. TrAp: Software: https://tinyheero.github.io/2015/08/26/TrAp.html
- 10. CITUP: Software: http://sourceforge.net/projects/citup/
- 11. CloneFinder: Software: https://github.com/gstecher/CloneFinderAPI
- 12. PhylogicNDT: Software: https://github.com/broadinstitute/PhylogicNDT
COSINE usage guidline: https://cunlab.org/2021/07/22/cosineusage0-1/
Python codes used in the support_manuscript(1).pdf
Computational Genomics & Medicine 