https://github.com/mrc-ide/mipanalyzer

Filtering and analysis of MIP data
https://github.com/mrc-ide/mipanalyzer

Last synced: about 2 months ago
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Filtering and analysis of MIP data

• Host: GitHub
• URL: https://github.com/mrc-ide/mipanalyzer
• Owner: mrc-ide
• License: mit
• Created: 2018-12-05T16:31:08.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2023-12-12T13:45:23.000Z (about 1 year ago)
• Last Synced: 2023-12-13T07:02:56.750Z (about 1 year ago)
• Language: R
• Homepage: https://mrc-ide.github.io/MIPanalyzer/
• Size: 7.6 MB
• Stars: 2
• Watchers: 4
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Awesome Lists containing this project

README

        
---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "README-"

)

```

[![develop checks](https://github.com/mrc-ide/PlasmoSim/workflows/checks_develop/badge.svg)](https://github.com/mrc-ide/PlasmoSim/actions)

[![master checks](https://github.com/mrc-ide/PlasmoSim/workflows/checks_master/badge.svg)](https://github.com/mrc-ide/PlasmoSim/actions)

MIPanalyzer

------------

`MIPanalyzer` is a tool for analyzing MIP (molecular inversion probe) data. It performs the following functions:

- Reading in raw data, usually in the form of a `vcf` file produced by [MIPwrangler](https://github.com/bailey-lab/MIPWrangler)

- Filtering samples and loci based on coverage, missingness, and other metrics

- Performing simple population genetic analyses, such as PCA and basic pairwise distance metrics

All documentation, including installation instructions and tutorials, are on [the MIPanalyzer website](https://mrc-ide.github.io/MIPanalyzer).

Version History

------------

The current release version of the software is v1.1.0, released 12 Dec 2023.

Contributors

------------

- [Bob Verity](https://github.com/bobverity)

- [OJ Watson](https://github.com/ojwatson)

- [Nick Brazeau](https://github.com/nickbrazeau)