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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# moiraine <img src="man/figures/logo.png" align="right" alt="" width="120" />
<!-- badges: start -->
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
<!-- badges: end -->
`moiraine` is a package for facilitating the construction of a reproducible analysis pipeline for multi-omics data integration. It provides functions to automate data import, pre-processing, transformation, integration through several tools, as well as interpretation and comparison of the integration results. It relies on the [targets](https://books.ropensci.org/targets/) package to generate reproducible workflows.
## Overview
The workflow for a typical multi-omics integration analysis handled with `moiraine` includes the following steps:
* Data import: this covers the import of omics measurements as well as associated metadata (i.e. information about the omics features and samples) -- moiraine relies on the [`MultiDataSet` package](https://bioconductor.org/packages/release/bioc/html/MultiDataSet.html) to store this information in a consistent format;
* Inspection of the omics datasets: including checking values density distribution, samples overlap between omics datasets, or presence of missing values;
* Preprocessing of the omics datasets: missing values imputation, transformation, and pre-filtering of samples and omics features;
* Integration of the omics datasets by one or more of the supported tools; currently, the following integration methods are covered in `moiraine`:
* sPLS and DIABLO from the `mixOmics` package
* sO2PLS from the `OmicsPLS` package
* MOFA and MEFISTO from the `MOFA2` package
* Interpretation of the integration results using standardised visualisations enriched with features and samples metadata;
* Comparison of the integration results obtained by different methods or pre-processing approaches.
An overview of the capabilities of the package is available [here](https://plant-food-research-open.github.io/moiraine-manual/overview.html).
## Installation
You can install the development version of moiraine from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("Plant-Food-Research-Open/moiraine")
```
## Example
To get started, create a new analysis pipeline in your working directory with:
```{r example}
#| eval: false
library(moiraine)
create_moiraine_pipeline()
```
The [user manual](https://plant-food-research-open.github.io/moiraine-manual/) provides an in-depth walk-through of a multi-omics integration analysis with the package.
Before using `moiraine`, we encourage you to get familiar with the `targets` package; the [`targets` manual](https://books.ropensci.org/targets/) is a great place to start.