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mcanouil committed May 11, 2021
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<!-- badges: start -->

[![Lifecycle: retired](https://img.shields.io/badge/lifecycle-retired-red.svg)](https://github.com/omicsr/CARoT)
[![Lifecycle: retired](https://img.shields.io/badge/lifecycle-retired-red.svg)](https://github.com/umr1283/CARoT)
[![GitHub
tag](https://img.shields.io/github/tag/omicsr/CARoT.svg?label=latest%20tag&include_prereleases)](https://github.com/omicsr/CARoT)
tag](https://img.shields.io/github/tag/umr1283/CARoT.svg?label=latest%20tag&include_prereleases)](https://github.com/umr1283/CARoT)
[![R build
status](https://github.com/omicsr/CARoT/workflows/R-CMD-check/badge.svg)](https://github.com/omicsr/CARoT/actions)
status](https://github.com/umr1283/CARoT/workflows/R-CMD-check/badge.svg)](https://github.com/umr1283/CARoT/actions)
<!-- badges: end -->

## Installation
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# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("omicsr/CARoT")
remotes::install_github("umr1283/CARoT")
```

``` r
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Currently *CARoT* includes the following functions from other packages:

- [`rain`](https://github.com/mcanouil/rain)
- [`rain`](https://github.com/umr1283/rain)
- `rain::estimate_ethnicity()` allows to format VCF files and
compute the genomic components (and some figures) for ethnicity
using [flashpca](https://github.com/gabraham/flashpca) software
Expand All @@ -60,12 +60,12 @@ Currently *CARoT* includes the following functions from other packages:
SNPS/genes and continuous or binary outcomes by including
variant characteristic information and using (weighted) score
statistics.
- [`dgapaq`](https://github.com/omicsr/dgapaq)
- [`dgapaq`](https://github.com/umr1283/dgapaq)
- `dgapaq::qc_plink()` allows to compute quality-control of
genotyping array (PLINK format) using a Rmarkdown template.
- `dgapaq::qc_vcf()` allows to compute post-imputation
quality-control report using a default Rmarkdown template.
- [`dmapaq`](https://github.com/omicsr/dmapaq)
- [`dmapaq`](https://github.com/umr1283/dmapaq)
- `dmapaq::ggheatmap()` allows to compute heatmap with dendrogram
on x-axis and y-axis using
[ggplot2](https://ggplot2.tidyverse.org/).
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## Getting help

If you encounter a clear bug, please file a minimal reproducible example
on [github](https://github.com/omicsr/CARoT/issues).
on [github](https://github.com/umr1283/CARoT/issues).
For questions and other discussion, please contact the package
maintainer.

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