https://github.com/umr1283/CARoT

Centralised and Automated RepOrting Tools
https://github.com/umr1283/CARoT

omics quality-control r r-package r-stats reporting

Last synced: 5 months ago
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Centralised and Automated RepOrting Tools

• Host: GitHub
• URL: https://github.com/umr1283/CARoT
• Owner: umr1283
• License: gpl-3.0
• Archived: true
• Created: 2019-04-12T12:34:23.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2021-09-15T22:03:50.000Z (over 3 years ago)
• Last Synced: 2024-08-13T07:14:08.581Z (8 months ago)
• Topics: omics, quality-control, r, r-package, r-stats, reporting
• Language: R
• Homepage:
• Size: 2.59 MB
• Stars: 2
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE.md
  • Code of conduct: .github/CODE_OF_CONDUCT.md
  • Support: .github/SUPPORT.md

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• jimsghstars - umr1283/CARoT - Centralised and Automated RepOrting Tools (R)

README

        
---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>"

)

```

# Centralised and Automated Reporting Tools 

[![Lifecycle: retired](https://img.shields.io/badge/lifecycle-retired-red.svg)](https://github.com/umr1283/CARoT)

[![GitHub tag](https://img.shields.io/github/tag/umr1283/CARoT.svg?label=latest tag&include_prereleases)](https://github.com/umr1283/CARoT)

[![R build status](https://github.com/umr1283/CARoT/workflows/R-CMD-check/badge.svg)](https://github.com/umr1283/CARoT/actions)

## Installation

```{r, eval = FALSE}

# Install CARoT from CRAN:

install.packages("CARoT")

# Or the the development version from GitHub:

# install.packages("remotes")

remotes::install_github("umr1283/CARoT")

```

```{r}

library(CARoT)

```

## Overview 

*CARoT* (Centralised and Automated Reporting Tools) is an under development set of Quality-Control reporting tools and some other functions.

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

* [`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

    - `rain::pca_report()` allows to compute an analysis report 

        using principal component analysis from 

        [flashpca](https://github.com/gabraham/flashpca) software.  

* [`MiSTr`](https://github.com/mcanouil/MiSTr)

    - `MiSTr::mist()` allows to test for association between 

    a set of SNPS/genes and continuous or binary outcomes by including variant 

    characteristic information and using (weighted) score statistics.

* [`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/umr1283/dmapaq)

    - `dmapaq::ggheatmap()` allows to compute heatmap with dendrogram on x-axis and y-axis 

        using [ggplot2](https://ggplot2.tidyverse.org/).

    - `dmapaq::read_idats()` allows to efficiently import idats files mostly 

        using [minfi](https://bioconductor.org/packages/minfi/) functions.

    - `dmapaq::qc_idats()` allows to compute quality-control of methylation array from Illumina 

        using a Rmarkdown template.

## Getting help

If you encounter a clear bug, please file a minimal reproducible example on [github](https://github.com/umr1283/CARoT/issues).  

For questions and other discussion, please contact the package maintainer.

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Please note that this project is released with a [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md).  

By participating in this project you agree to abide by its terms.