tima

Requirements

Here is what you minimally need:

• A feature list (.csv) (see example features)
• A spectral file corresponding to the feature list (.mgf) (see example spectra)
• The biological source(s) of the sample(s) you are annotating (.csv) (see example metadata) (File is optional if only a single organism)

Optionally, you may want to add:

• An in-house structure-organism pairs library (we provide LOTUS as starting point for each user)
• Your own manual or automated annotations (we currently support annotations coming from SIRIUS (with some limitations))

Installation

As the package is not (yet) available on CRAN, you will need to install with:

install.packages(
  "tima",
  repos = c(
    "https://taxonomicallyinformedannotation.r-universe.dev",
    "https://bioc.r-universe.dev",
    "https://cloud.r-project.org"
  )
)

Then, you should be able to install the rest with:

tima::install()

Normally, everything you need should then be installed (as tested in here). If for some reason, some packages were not installed, try to install them manually. To avoid such issues, we offer a containerized version (see Docker).

Once installed, you are ready to go through our documentation, with the major steps detailed.

In case you do not have your data ready, you can obtain some example data using:

tima::get_example_files()

Once you are done, you can open a small GUI to adapt your parameters and launch your job:

tima::run_app()

This command will open a small app in your default browser.

docker pull adafede/tima-r
# docker build . -t adafede/tima-r

docker run --user tima-user -v "$(pwd)/.tima/data:/home/tima-user/.tima/data" -p 3838:3838 adafede/tima-r Rscript -e "tima::run_app()"
# docker run --user tima-user -v "$(pwd)/.tima/data:/home/tima-user/.tima/data" adafede/tima-r Rscript -e "tima::tima_full()"

Main Citations

According to which steps you used, please give credit to the authors of the tools/resources used.