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| ^CRAN-RELEASE$ | ||
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| This package was submitted to CRAN on 2019-01-10. | ||
| Once it is accepted, delete this file and tag the release (commit 1b7b7604fc). |
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| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
| sigminer | ||
| ======== | ||
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| <img src="https://github.com/ShixiangWang/sigminer/blob/master/inst/figures/sigminer.png" height="200" align="right" /> | ||
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| [](https://cran.r-project.org/package=sigminer) [](https://www.tidyverse.org/lifecycle/#maturing) [](https://ci.appveyor.com/project/ShixiangWang/sigminer) [](https://travis-ci.org/ShixiangWang/sigminer) [](https://codecov.io/github/ShixiangWang/sigminer?branch=master) | ||
| # sigminer | ||
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| The goal of **sigminer** is to provide an uniform interface for genomic variation signature analysis and visualization. **sigminer** is originated from [VSHunter](https://github.com/ShixiangWang/VSHunter) package I wrote. I hate ugly structure and function names in VSHunter, thus reconstruct it using concise function names, S4 classes and S3 methods etc.. I will continue to add more features to uncover genomic variation signatures and their correlationship with phenotyes and genotypes. | ||
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| **sigminer** is powered by [NMF](https://github.com/renozao/NMF) package and [maftools](https://github.com/PoisonAlien/maftools) package. | ||
| <img src="https://github.com/ShixiangWang/sigminer/blob/master/inst/figures/sigminer.png" height="200" align="right" /> | ||
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| Installation | ||
| ------------ | ||
| [](https://cran.r-project.org/package=sigminer) | ||
| [](https://www.tidyverse.org/lifecycle/#maturing) | ||
| [](https://ci.appveyor.com/project/ShixiangWang/sigminer) | ||
| [](https://travis-ci.org/ShixiangWang/sigminer) | ||
| [](https://codecov.io/github/ShixiangWang/sigminer?branch=master) | ||
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| The goal of **sigminer** is to provide an uniform interface for genomic | ||
| variation signature analysis and visualization. **sigminer** is | ||
| originated from [VSHunter](https://github.com/ShixiangWang/VSHunter) | ||
| package I wrote. I hate ugly structure and function names in VSHunter, | ||
| thus reconstruct it using concise function names, S4 classes and S3 | ||
| methods etc.. I will continue to add more features to uncover genomic | ||
| variation signatures and their correlationship with phenotypes and | ||
| genotypes. | ||
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| **sigminer** is powered by [NMF](https://github.com/renozao/NMF) package | ||
| and [maftools](https://github.com/PoisonAlien/maftools) package. | ||
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| ## Installation | ||
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| You can install the development version of sigminer from Github with: | ||
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| ``` r | ||
| devtools::install_github("ShixiangWang/sigminer") | ||
| ``` | ||
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| Citation | ||
| -------- | ||
| ## Citation | ||
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| - *Macintyre, Geoff, et al. “Copy number signatures and mutational processes in ovarian carcinoma.” Nature genetics 50.9 (2018): 1262.* | ||
| - *Macintyre, Geoff, et al. “Copy number signatures and mutational | ||
| processes in ovarian carcinoma.” Nature genetics 50.9 (2018): 1262.* | ||
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| - *Wang, Shixiang, et al. “APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer.” Oncogene (2018).* | ||
| - *Wang, Shixiang, et al. “APOBEC3B and APOBEC mutational signature as | ||
| potential predictive markers for immunotherapy response in non-small | ||
| cell lung cancer.” Oncogene (2018).* | ||
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| TODO | ||
| ---- | ||
| ## TODO | ||
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| - survival analysis, including | ||
| - Cox | ||
| - KM | ||
| - survival analysis, including | ||
| - Cox | ||
| - KM |