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Neuroconductor and R image analysis packages.

  • About Neuroconductor

     

    Neuroconductor is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to:

    • provide a centralized repository of R software dedicated to image analysis;
    • disseminate quickly software updates;
    • educate a large, diverse community of scientists using detailed tutorials and short courses;
    • ensure quality via automatic and manual quality controls; and
    • promote reproducibility of image data analysis.

    Based on the programming language R, Neuroconductor started with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing.

     

    webpage : https://neuroconductor.org/

     

    Installing Neuroconductor Packages

     

    Install and start the latest release version of R. Although the installer will try to download and install devtools, there may be some system requirements for devtools that you may need before going forward. Please visit installing devtools before going forward if you do not have devtools currently installed.

    Then, you can install a package using the following command:

    ## try http:// if https:// URLs are supported
    source("https://neuroconductor.org/neurocLite.R")
    neuro_install("PACKAGE")

    where PACKAGE is the name of the package you’d like to install, such as fslr. For example, if we want to install neurohcp and fslr we can run:

    source("https://neuroconductor.org/neurocLite.R")
    neuro_install(c("fslr", "neurohcp"))

     

    Installing the neurocInstall package

     

    The neurocInstall package contains the neurocLite/neuro_install functions, as well as others relevant for Neuroconductor. You can install the package as follows:

     

    source("https://neuroconductor.org/neurocLite.R")
    neuro_install("neurocInstall")

     

    After installation, you can use neurocInstall::neurocLite() to install packages without source-ing the URL above.

     

    Installing Stable/Current/Release Versions

     

    Stable Versions

     

    In Neuroconductor, there are stable versions, which correspond to a submitted package. This stable version has passed the Neuroconductor checks on Travis for Linux using the other packages in Neuroconductor that are in Neuroconductor at the time of submission. Thus, if you install this package with all the dependencies listed for this package (using specific Neuroconductor versions), it should work.

     

    To install a stable version (which should be the default), you can run:

     

    source("https://neuroconductor.org/neurocLite.R")
    neuro_install(c("fslr", "neurohcp"), release = "stable")

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