From e097c606d37461ef5188dca2df0365da427554dc Mon Sep 17 00:00:00 2001 From: ShixiangWang Date: Thu, 10 Jan 2019 16:13:14 +0800 Subject: [PATCH] submit to CRAN --- .Rbuildignore | 1 + CRAN-RELEASE | 2 ++ README.Rmd | 2 +- README.md | 54 +++++++++++++++++++++++++++++++++------------------ 4 files changed, 39 insertions(+), 20 deletions(-) create mode 100644 CRAN-RELEASE diff --git a/.Rbuildignore b/.Rbuildignore index eac157d0..a3d8f02e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,4 @@ +^CRAN-RELEASE$ ^codecov\.yml$ ^\.travis\.yml$ ^appveyor\.yml$ diff --git a/CRAN-RELEASE b/CRAN-RELEASE new file mode 100644 index 00000000..f495ffe5 --- /dev/null +++ b/CRAN-RELEASE @@ -0,0 +1,2 @@ +This package was submitted to CRAN on 2019-01-10. +Once it is accepted, delete this file and tag the release (commit 1b7b7604fc). diff --git a/README.Rmd b/README.Rmd index aa600da6..7c9304c8 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,7 +20,7 @@ knitr::opts_chunk$set( [![CRAN status](https://www.r-pkg.org/badges/version/sigminer)](https://cran.r-project.org/package=sigminer) [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/ShixiangWang/sigminer?branch=master&svg=true)](https://ci.appveyor.com/project/ShixiangWang/sigminer) [![Travis build status](https://travis-ci.org/ShixiangWang/sigminer.svg?branch=master)](https://travis-ci.org/ShixiangWang/sigminer) [![Coverage status](https://codecov.io/gh/ShixiangWang/sigminer/branch/master/graph/badge.svg)](https://codecov.io/github/ShixiangWang/sigminer?branch=master) -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. +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. **sigminer** is powered by [NMF](https://github.com/renozao/NMF) package and [maftools](https://github.com/PoisonAlien/maftools) package. diff --git a/README.md b/README.md index 3ee52e10..b1b05f80 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,33 @@ -sigminer -======== - - -[![CRAN status](https://www.r-pkg.org/badges/version/sigminer)](https://cran.r-project.org/package=sigminer) [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/ShixiangWang/sigminer?branch=master&svg=true)](https://ci.appveyor.com/project/ShixiangWang/sigminer) [![Travis build status](https://travis-ci.org/ShixiangWang/sigminer.svg?branch=master)](https://travis-ci.org/ShixiangWang/sigminer) [![Coverage status](https://codecov.io/gh/ShixiangWang/sigminer/branch/master/graph/badge.svg)](https://codecov.io/github/ShixiangWang/sigminer?branch=master) +# sigminer -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. - -**sigminer** is powered by [NMF](https://github.com/renozao/NMF) package and [maftools](https://github.com/PoisonAlien/maftools) package. + -Installation ------------- +[![CRAN +status](https://www.r-pkg.org/badges/version/sigminer)](https://cran.r-project.org/package=sigminer) +[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) +[![AppVeyor build +status](https://ci.appveyor.com/api/projects/status/github/ShixiangWang/sigminer?branch=master&svg=true)](https://ci.appveyor.com/project/ShixiangWang/sigminer) +[![Travis build +status](https://travis-ci.org/ShixiangWang/sigminer.svg?branch=master)](https://travis-ci.org/ShixiangWang/sigminer) +[![Coverage +status](https://codecov.io/gh/ShixiangWang/sigminer/branch/master/graph/badge.svg)](https://codecov.io/github/ShixiangWang/sigminer?branch=master) + +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. + +**sigminer** is powered by [NMF](https://github.com/renozao/NMF) package +and [maftools](https://github.com/PoisonAlien/maftools) package. + +## Installation You can install the development version of sigminer from Github with: @@ -20,16 +35,17 @@ You can install the development version of sigminer from Github with: devtools::install_github("ShixiangWang/sigminer") ``` -Citation --------- +## Citation -- *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.* -- *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).* -TODO ----- +## TODO -- survival analysis, including -- Cox -- KM + - survival analysis, including + - Cox + - KM