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Please edit that file --\u003e\n\n```{r setup, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"README-\",\n  fig.width = 6,\n  fig.height = 5\n)\n```\n\n# Spectroscopy Analysis Tools (spant) \u003cimg src=\"man/figures/logo.png\" align=\"right\" width=130/\u003e\n[![R_build_status](https://github.com/martin3141/spant/workflows/R-CMD-check/badge.svg)](https://github.com/martin3141/spant/actions)\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.03646/status.svg)](https://doi.org/10.21105/joss.03646)\n[![CRAN_status_badge](https://www.r-pkg.org/badges/version/spant)](https://cran.r-project.org/package=spant)\n[![Downloads](https://cranlogs.r-pkg.org/badges/last-month/spant)](https://cran.r-project.org/package=spant)\n\n## Overview\n\nspant provides a full suite of tools to build automated analysis pipelines for Magnetic Resonance Spectroscopy (MRS) data. The following features and algorithms are included:\n\n* Advanced fully-automated metabolite fitting algorithm - ABfit https://onlinelibrary.wiley.com/doi/10.1002/mrm.28385, https://onlinelibrary.wiley.com/doi/10.1002/mrm.30462.\n* Robust retrospective frequency and phase correction - RATS https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.27605.\n* Support for common MRS data formats including read / write NIfTI MRS - https://onlinelibrary.wiley.com/doi/10.1002/mrm.29418.\n* Flexible data types to support single voxel, dynamic and spectroscopic imaging.\n* Raw data import from individual coils and dynamic measurements, eg support for importing individual FIDs from Siemens TWIX formatted data.\n* Publication quality plotting.\n* Extensive set of pre-processing steps (phasing, coil-combination, zero-filling, HSVD filtering...).\n* Quantum mechanical based simulation for experimental design and basis-set generation.\n* Set of metabolite, macromolecule and lipid parameters for typical brain analyses.\n* Voxel registration to anatomical images for partial volume concentration corrections.\n\n## Documentation\n\nThe [online spant user manual](https://spantdoc.wilsonlab.co.uk/) ([pdf version](https://spantdoc.wilsonlab.co.uk/spant-User-Manual.pdf)) is written for users with minimal experience in R or MRS processing and is the best place to start.\n\nFor more advanced users, help developing custom analysis pipeline can be found\nbelow.\n\nIntroduction : https://martin3141.github.io/spant/articles/spant-intro.html\n\nShort tutorials : https://martin3141.github.io/spant/articles/\n\nFunction reference : https://martin3141.github.io/spant/reference/\n\nOnce 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`.\n\n## Basic installation\n\nDownload 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`.\n\nIt is also strongly recommended to install RStudio Desktop (https://rstudio.com/products/rstudio/download) to provide a modern environment for interactive data analysis.\n\nOnce 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:\n```{r cran, eval = FALSE}\ninstall.packages(\"spant\", dependencies = TRUE)\n```\n\nOr the the development version from GitHub (requires the `devtools` package):\n```{r github, eval = FALSE}\ninstall.packages(\"devtools\")\ndevtools::install_github(\"martin3141/spant\", ref = \"devel\", dependencies = TRUE)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmartin3141%2Fspant","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmartin3141%2Fspant","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmartin3141%2Fspant/lists"}