README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r setup, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-",
  fig.width = 6,
  fig.height = 5,
  dev = "ragg_png"
)
```

# Spectroscopy Analysis Tools (spant) <img src="man/figures/logo.png" align="right" width=130/>
[![R build status](https://github.com/martin3141/spant/workflows/R-CMD-check/badge.svg)](https://github.com/martin3141/spant/actions)
[![](http://cranlogs.r-pkg.org/badges/spant)](http://cran.rstudio.com/web/packages/spant/index.html)
[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/spant)](https://cran.r-project.org/package=spant)
[![Coverage Status](https://coveralls.io/repos/github/martin3141/spant/badge.svg?branch=master)](https://coveralls.io/github/martin3141/spant?branch=master)

## Overview
spant provides a full suite of tools to build automated analysis pipelines for
Magnetic Resonance Spectroscopy (MRS) data. The following features and
algorithms are included:

* Advanced fully-automated metabolite fitting algorithm - ABfit (in-press at Magnetic Resonance in Medicine) https://onlinelibrary.wiley.com/doi/10.1002/mrm.28385.
* Robust retrospective frequency and phase correction - RATS https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.27605.
* Flexible data types to support single voxel, dynamic and spectroscopic imaging data types.
* Raw data import/export.
* Publication quality plotting.
* Extensive set of pre-processing steps (phasing, coil-combination, zero-filling, HSVD filtering...)
* Quantum mechanical based simulation for experimental design and basis-set generation.
* Set of metabolite, macromolecule and lipid parameters for typical brain analyses.
* Voxel registration to anatomical images for partial volume concentration corrections.

## Installation
Download and install the latest version of R (https://cloud.r-project.org/), or with your package manager if using a recent Linux distribution, eg `sudo apt install r-base`.

It is also strongly recommended to install RStudio Desktop (https://rstudio.com/products/rstudio/download) to provide a modern environment for interactive data analysis.

Once R and RStudio have been installed, open the RStudio application and type the following in the Console (lower left panel) to install the latest stable version of spant:
```{r cran, eval = FALSE}
install.packages("spant", dependencies = TRUE)
```

Or the the development version from GitHub (requires the `devtools` package):
```{r github, eval = FALSE}
install.packages("devtools")
devtools::install_github("martin3141/spant", ref = "devel")
```

## Documentation
Quick introduction to the basic analysis workflow : https://martin3141.github.io/spant/articles/spant-intro.html

Short tutorials : https://martin3141.github.io/spant/articles/

Function reference : https://martin3141.github.io/spant/reference/

Once the spant library has been loaded with `library(spant)`, type `?spant` on the console for instructions on how to access the offline documentation. Note that offline help on the available functions can be quickly shown in RStudio using `?function_name`, eg `?read_mrs`.