| Item | Link |
|---|---|
| CNV_pipeline | https://github.com/navinlabcode/CNV_pipeline |
| Item | Purpose | Link |
|---|---|---|
| R language (4.1.2) | programing | https://www.r-project.org/ |
| scATAC-pro | ATAC | https://github.com/wbaopaul/scATAC-pro |
| ArchR | ATAC | https://github.com/GreenleafLab/ArchR |
| Signac | ATAC | https://stuartlab.org/signac/ |
| Cicero | ATAC | https://github.com/cole-trapnell-lab/cicero |
| Copykit | CNA | https://github.com/navinlabcode/copykit |
| ggtree | visualization | https://www.bioconductor.org/packages/release/bioc/html/ggtree.html |
| ComplexHeatmap | visualization | https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html |
| ggpubr | visualization | https://rpkgs.datanovia.com/ggpubr/ |
| Item | Purpose | Link |
|---|---|---|
| Python (3.10.12) | programing | https://www.anaconda.com/download |
| MEDICC2 | CNA | https://bitbucket.org/schwarzlab/medicc2/src/master/ |