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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# MPTevol
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Multiple primary tumors (MPT) is a special and rare cancer type, defined as more than two primary tumors presenting at the diagnosis in a single patient. The molecular characteristics and tumorigenesis of MPT remain unclear due to insufficient approaches.
Here, we present `MPTevol`, a practical computational framework for comprehensively exploring the MPT from **multiregional sequencing (MRS)** experiments. `MPTevol` facilitates comparison genomic profiles across multiple primary tumor samples, detection of clonal evolutionary history and metastatic routines in MPT, and quantification of metastatic history. This package incorporates multiple cancer evolution analyses, for a one-stop solution of MPT analysis.The goal of MPTevol is to provide a practical computation framework for dissecting the evolution of multiple primary tumors (MPT), reducing analysis complexity with modular design.
## Package Overview
## Citations
If you are using the MPTevol in academic research, please cite our paper:
**Chen, Q., Wu, Q.-N., Rong, Y.-M., Wang, S., Zuo, Z., Bai, L., . . . Zhao, Q. (2022). [Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol](https://doi.org/10.1093/bib/bbac175). Briefings in Bioinformatics. doi:10.1093/bib/bbac175**
## Installation
You can install the development version of MPTevol from [GitHub](https://github.com/) with:
``` r
# install.packages("remotes")
remotes::install_github("qingjian1991/MPTevol")
```
## Documentation
The overview of usage could be found at [MPTevol online vignette](https://rpubs.com/cqj_00/MPTevol).
## Package structure
## Authors
This software is developed by:
* Qingjian Chen, <[email protected]>, Sun Yat-Sen Univerity Cancer Center.
* Shixiang Wang, <[email protected]>, Sun Yat-Sen Univerity Cancer Center.
## Supervised by
* [Qi Zhao]([email protected]) from Bioinformatic Center of Sun Yat-sen University Cancer Center.