Table 2.
Summary of advanced tools
| Tools | Language | Method | Download | Cite | |
|---|---|---|---|---|---|
| 1 | SC3 | R | Cluster | https://github.com/hemberg-lab/sc3 | 10.1101/036558; 10.1038/nmeth.4236 |
| 2 | SCENIC | R/Python | Cluster | https://github.com/aertslab/SCENIC | 10.1101/144501; 10.1038/nmeth.4463 |
| 3 | BackSPIN | Python | Bicluster | https://github.com/linnarsson-lab/BackSPIN | 10.1126/science.aaa1934 |
| 4 | BiSNN-Walk | / | Bicluster | / | 10.1089/cmb.2017.0049 |
| 5 | SNN-Cliq | MATLAB/Python | Cluster | http://bioinfo.uncc.edu/SNNCliq | 10.1093/bioinformatics/btv088 |
| 6 | NMF | Python | Cluster | https://github.com/ccshao/nimfa | 10.1093/bioinformatics/btw607 |
| 7 | SIMLR | MATLAB | ML+cluster | https://github.com/BatzoglouLabSU/SIMLR | 10.1038/nmeth.4207 |
| 8 | SINCERA | R | Cluster | https://github.com/xu-lab/SINCERA | 10.1371/journal.pcbi.1004575; 10.1007/978-1-4939-7710-9_15 |
| 9 | SEURAT | R | Cluster | https://github.com/satijalab/seurat | 10.1038/nbt.3192; 10.1101/164889 |
| 10 | Monocle | R | Cluster | https://github.com/cole-trapnell-lab/monocle-release | 10.1038/nbt.2859; 10.1038/nmeth.4150; 10.1101/110668; 10.1038/nmeth.4402 |
| 11 | SCRL | C++ | ML+cluster |
https://github.com/SuntreeLi/
SCRL |
10.1093/nar/gkx750 |