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spant

spant: An R package for magnetic resonance spectroscopy analysis - Published in JOSS (2021)

https://github.com/martin3141/spant

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: wiley.com, joss.theoj.org
  • ✓
    Committers with academic emails
    2 of 6 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

brain cran mri mrs mrshub spectroscopy
Last synced: 4 months ago · JSON representation

Repository

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data

Basic Info
Statistics
  • Stars: 27
  • Watchers: 4
  • Forks: 6
  • Open Issues: 0
  • Releases: 67
Topics
brain cran mri mrs mrshub spectroscopy
Created about 9 years ago · Last pushed 5 months ago
Metadata Files
Readme Changelog Contributing License

README.Rmd 

---
output: github_document
---



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

# Spectroscopy Analysis Tools (spant) 
[![R_build_status](https://github.com/martin3141/spant/workflows/R-CMD-check/badge.svg)](https://github.com/martin3141/spant/actions)
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03646/status.svg)](https://doi.org/10.21105/joss.03646)
[![CRAN_status_badge](https://www.r-pkg.org/badges/version/spant)](https://cran.r-project.org/package=spant)
[![Downloads](https://cranlogs.r-pkg.org/badges/last-month/spant)](https://cran.r-project.org/package=spant)

## 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 https://onlinelibrary.wiley.com/doi/10.1002/mrm.28385, https://onlinelibrary.wiley.com/doi/10.1002/mrm.30462.
* Robust retrospective frequency and phase correction - RATS https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.27605.
* Support for common MRS data formats including read / write NIfTI MRS - https://onlinelibrary.wiley.com/doi/10.1002/mrm.29418.
* Flexible data types to support single voxel, dynamic and spectroscopic imaging.
* Raw data import from individual coils and dynamic measurements, eg support for importing individual FIDs from Siemens TWIX formatted data.
* 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.

## Documentation

The [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.

For more advanced users, help developing custom analysis pipeline can be found
below.

Introduction : 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`.

## Basic 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", dependencies = TRUE)
```

Owner

  • Name: Martin Wilson
  • Login: martin3141
  • Kind: user
  • Location: Birmingham
  • Company: University of Birmingham

MR Physicist at CHBH, University of Birmingham

JOSS Publication

spant: An R package for magnetic resonance spectroscopy analysis
Published
November 02, 2021
DOI
Volume 6, Issue 67, Page 3646
Authors
Martin Wilson ORCID
Centre for Human Brain Health and School of Psychology, University of Birmingham, Birmingham, UK
Editor
Chris Hartgerink ORCID
Tags
spectroscopy MRS NMR medical imaging neuroimaging
View PDF Review Thread Software Archive

Papers & Mentions

Total mentions: 1

Mapping of Metabolic Heterogeneity of Glioma Using MR-Spectroscopy
Last synced: 3 months ago

GitHub Events

Total
  • Create event: 5
  • Issues event: 2
  • Release event: 4
  • Watch event: 4
  • Issue comment event: 4
  • Push event: 194
Last Year
  • Create event: 5
  • Issues event: 2
  • Release event: 4
  • Watch event: 4
  • Issue comment event: 4
  • Push event: 194

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 1,993
  • Total Committers: 6
  • Avg Commits per committer: 332.167
  • Development Distribution Score (DDS): 0.011
Past Year
  • Commits: 258
  • Committers: 1
  • Avg Commits per committer: 258.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Martin Wilson m****n@p****k 1,971
muschellij2 m****2@g****m 9
Martin Wilson (Psychology) m****n@b****k 9
alexcraven 1****n 2
Martin Wilson m****n@M****l 1
Martin Wilson m****n@B****K 1
Committer Domains (Top 20 + Academic)
buic-pc6.bham.ac.uk: 1 bham.ac.uk: 1 pipegrep.co.uk: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 9
  • Total pull requests: 4
  • Average time to close issues: 5 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 6
  • Total pull request authors: 2
  • Average comments per issue: 2.56
  • Average comments per pull request: 0.5
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: about 22 hours
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • slieped (3)
  • TKoscik (2)
  • jonclayden (1)
  • grandjeanlab (1)
  • joaomcteixeira (1)
  • teddychao (1)
Pull Request Authors
  • muschellij2 (3)
  • alexcraven (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,077 last-month
  • Total docker downloads: 20,358
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 70
  • Total maintainers: 1
cran.r-project.org: spant

MR Spectroscopy Analysis Tools

  • Versions: 70
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 1,077 Last month
  • Docker Downloads: 20,358
Rankings
Forks count: 10.1%
Stargazers count: 12.6%
Downloads: 15.8%
Average: 20.7%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
martin@pipegrep.co.uk
Last synced: 4 months ago

Dependencies

.github/workflows/check-standard.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 2.10 depends
  • RNifti * imports
  • RNiftyReg * imports
  • abind * imports
  • expm * imports
  • fields * imports
  • grDevices * imports
  • graphics * imports
  • irlba * imports
  • jsonlite * imports
  • minpack.lm * imports
  • mmand * imports
  • nloptr * imports
  • numDeriv * imports
  • plyr * imports
  • pracma * imports
  • ptw * imports
  • signal * imports
  • smoother * imports
  • stringr * imports
  • utils * imports
  • doParallel * suggests
  • knitr * suggests
  • miniUI * suggests
  • ragg * suggests
  • rmarkdown * suggests
  • shiny * suggests
  • testthat * suggests
  • viridisLite * suggests