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TARDIS

R package for TArgeted Raw Data Integration In Spectrometry

Installation

Make sure R (version >= 4.4.0) is installed on your computer:

https://cloud.r-project.org/index.html

For Windows users, Rtools should be installed as well:

https://cran.r-project.org/bin/windows/Rtools/rtools44/rtools.html

For Mac users, please install Xcode and a GNU Fortran compiler, see: https://mac.r-project.org/tools/index.html For Xcode, you can run this line in your Mac OS terminal:

sudo xcode-select --install

For the latest version of TARDIS, BiocManager version 3.20 is required: https://www.bioconductor.org/install/

In R, run:

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pablovgd/TARDIS",build_vignettes = FALSE,
  dependencies=TRUE)

Since the package contains some example data, connection timeout is often an issue. You can increase your timeout setting in R using:

options(timeout = "300")

The number indicates the timeout setting in seconds.

Usage

Load the package:

library(TARDIS)

Read the vignettes for a tutorial on how to use TARDIS

Available online: https://pablovgd.github.io/TARDIS/

Or, if you installed with build_vignettes = TRUE

RShowDoc("quick_start",package = "TARDIS")
RShowDoc("gui_tutorial",package = "TARDIS")
RShowDoc("case_study",package = "TARDIS")

To launch the GUI in R:

runTardis()

TARDIS is licensed under the GPLv3

As a summary, the GPLv3 license requires attribution, inclusion of copyright and license information, disclosure of source code and changes. Derivative work must be available under the same terms.

  1. Pablo Vangeenderhuysen (2024)