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tacmagic

tacmagic: Positron emission tomography analysis in R - Published in JOSS (2019)

https://github.com/ropensci/tacmagic

Science Score: 93.0%

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

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 5 DOI reference(s) in README and JOSS metadata
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    Links to: joss.theoj.org, zenodo.org
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    Published in Journal of Open Source Software

Keywords

mri neuroimaging neuroscience neuroscience-methods pet pet-mr positron positron-emission-tomography r statistics
Last synced: 6 months ago · JSON representation

Repository

tacmagic: PET Analysis in R

Basic Info
Statistics
  • Stars: 6
  • Watchers: 5
  • Forks: 1
  • Open Issues: 1
  • Releases: 5
Topics
mri neuroimaging neuroscience neuroscience-methods pet pet-mr positron positron-emission-tomography r statistics
Created almost 8 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog Contributing License Codemeta

README.md

tacmagic: PET Analysis in R

DOI Build Status Coverage status JOSS

To foster openness, replicability, and efficiency, tacmagic facilitates loading and analysis of positron emission tomography data in R.

As a tacmagic is a new package, we strongly recommend checking all work against existing analyses to confirm the results are as expected, and welcome any feedback.

Installation

The stable version of the package can be installed from CRAN, and the more recent development version can be installed with the devtools package.

Use the following R commands to download the version you would like: for the CRAN release, install.packages("tacmagic"), for the github release version that may not yet be available on CRAN, devtools::install_github("ropensci/tacmagic"), and for the very latest in-development version that is more likely to have bugs or errors and thus is not suitable for production use, use devtools::install_github("ropensci/tacmagic", ref="devel").

Features

The features of tacmagic are demonstrated in the package's walkthrough vignette, which is highly recommended for first-time uses.

Data loading and weighted-averages

Time-activity curve (TAC) and/or region of interest (ROI) volume data can be loaded from various file formats including PMOD .tac and .voistat files, a .mat file from the magia pipeline, and Turku PET Centre's .DFT format.

There is support for converting the radioactivity units in TAC data.

This package is not affiliated with any of the above pipelines.

Time-activity curve plotting

Basic plotting of one or more TAC from one or more participants is available.

Binding potential models

Non-invasive models are implemented including the standardized uptake volume (SUV), SUV ratio (SUVR), and the non-invasive Logan reference method.

Batch and group-wise analysis

Loading and analysis functions can be run as a batch or by individual participant.

Licence

Copyright (C) 2018 Eric E. Brown

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

We also note specifically that this package is not intended for clinical use, and may contain bugs or errors, so any results should be verified. As above, we provide no warranty and assume no liability.

Citation

Please cite this software package if you use it in your analyses.

Brown, E. E. (2019). tacmagic: PET Analysis in R. Journal of Open Source Software, 4(34), 1281. doi:10.21105/joss.01281.

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Owner

  • Name: rOpenSci
  • Login: ropensci
  • Kind: organization
  • Email: info@ropensci.org
  • Location: Berkeley, CA

JOSS Publication

tacmagic: Positron emission tomography analysis in R
Published
February 27, 2019
DOI
Volume 4, Issue 34, Page 1281
Authors
Eric E. Brown ORCID
Department of Psychiatry and Institute of Medical Science, University of Toronto, Toronto, Canada, Centre for Addiction and Mental Health, Toronto, Canada
Editor
Daniel S. Katz ORCID
Tags
positron emission tomography biomedical imaging neuroimaging neuroscience neuroinformatics
View PDF Review Thread Software Archive

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Packages

  • Total packages: 1
  • Total downloads:
    • cran 214 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: tacmagic

Positron Emission Tomography Time-Activity Curve Analysis

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 214 Last month
Rankings
Forks count: 21.9%
Stargazers count: 26.2%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 36.5%
Downloads: 69.4%
Maintainers (1)
eb@ericebrown.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.4 depends
  • R.matlab * imports
  • grDevices * imports
  • graphics * imports
  • pracma * imports
  • utils * imports
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • vdiffr * suggests