In addition to developing methods single-cell genomics, our lab has built analytical packages for other biological settings:
1. Canopy: Canopy is a statistical framework to reconstruct tumor phylogeny by next-generation sequencing data from temporally and/or spatially separated tumor resections from the same patient.
Canopy is an open-source R package available at https://cran.r-project.org/web/packages/Canopy/.
2. DNA copy number analysis and tumor heterogeneity profiling
You should first read the MARATHON paper (Urrutia et al., 2018) to get a sense of whether you should use iCNV, CODEX, CODEX2, FALCON, or FALCON-X for your data.
- MARATHON: Comprehensive pipeline for copy number profiling in normal and tumor samples and phylogeny inference in tumor samples. The website for Marathon includes a comprehensive tutorial on the entire pipeline.
https://github.com/yuchaojiang/MARATHON
- CODEX/CODEX2: A statistical framework for full-spectrum CNV profiling in whole genome, whole exome, and targeted DNA sequencing data that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples.
https://github.com/yuchaojiang/CODEX2
- iCNV: iCNVis a normalization and copy number variation detection procedure for mutiple study designs: WES only, WGS only, SNP array only, or any combination of SNP and sequencing data. iCNV applies platform specific normalization, utilizes allele specific reads from sequencing and integrates matched NGS and SNP-array data by a Hidden Markov Model (HMM).
https://github.com/zhouzilu/iCNV
- FALCON/FALCON-X: Allele-specific DNA Copy Number profiling for whole-genome sequencing data (FALCON) and whole-exome sequencing data (FALCON-X). You may find it helpful to first read the Marathon paper (above), which describes how these stand-alone software can be combined with other tools.
https://cran.r-project.org/web/packages/falcon/index.html
https://cran.r-project.org/web/packages/falconx/index.html