README.qmd

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# CASCADE <img src='https://raw.githubusercontent.com/adafede/cascade/main/man/figures/logo.svg' align="right" height="139" />

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**C**ontextualizing untargeted **A**nnotation with **S**emi-quantitative
**C**harged **A**erosol **D**etection for pertinent characterization of natural
**E**xtracts.

⚠️ This repository is not maintained and will not be except for extreme
interest. It has just been opened for the sake of transparency.

The initial work is available at https://doi.org/10.1021/acs.jafc.3c03099, with
some improvements made since then. The workflow is illustrated below.

![Workflow](https://raw.githubusercontent.com/adafede/cascade/main/man/figures/cascade-workflow.svg)
\

## Requirements

Here is what you *minimally* need:

- A file
  ([.mzML](https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#mzML))
  containing [DDA
  MS](https://en.wikipedia.org/w/index.php?title=Data-dependent_acquisition)
  data with an additional detector
  ([PDA](https://en.wikipedia.org/wiki/UV_detectors),
  [ELSD](https://en.wikipedia.org/wiki/Evaporative_light_scattering_detector),
  [CAD](https://en.wikipedia.org/wiki/Charged_aerosol_detector))
  - In case you don't know how to obtain it, see:
    [wiki/How-to-create-a-compliant-mzML-file](https://github.com/Adafede/cascade/wiki/How-to-create-a-compliant-mzML-file)
- A file ([.csv](https://en.wikipedia.org/wiki/Comma-separated_values))
  containing features, as obtained by [mzmine](https://mzio.io)
- A file ([.tsv](https://en.wikipedia.org/wiki/Tab-separated_values)) containing
  annotations, as obtained by
  [TIMA](https://taxonomicallyinformedannotation.github.io/tima)

## Installation

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

```r
install.packages(
  "cascade",
  repos = c(
    "https://adafede.r-universe.dev",
    "https://taxonomicallyinformedannotation.r-universe.dev",
    "https://cran.r-universe.dev",
    "https://bioc.r-universe.dev"
  )
)
```

Once installed, you are ready to go through our
[documentation](https://adafede.github.io/cascade/articles), with the major
steps detailed.

## Main Citations

### CASCADE

<https://doi.org/10.1021/acs.jafc.3c03099>

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

### mzmine

General: <https://doi.org/10.1038/s41587-023-01690-2>

### SIRIUS

General: <https://doi.org/10.1038/s41592-019-0344-8>

- *CSI:FingerId*: <https://doi.org/10.1073/pnas.1509788112>
- *ZODIAC*: <https://doi.org/10.1038/s42256-020-00234-6>
- *CANOPUS*: <https://doi.org/10.1038/s41587-020-0740-8>
- *COSMIC*: <https://doi.org/10.1038/s41587-021-01045-9>

### LOTUS

General: <https://doi.org/10.7554/eLife.70780>

⚠️ Do not forget to cite which version you used:
<https://doi.org/10.5281/zenodo.5794106>

### ISDB

General: <https://doi.org/10.1021/acs.analchem.5b04804>

⚠️ Do not forget to cite which version you used:
<https://doi.org/10.5281/zenodo.5607185>

### TIMA

General: <https://doi.org/10.3389/fpls.2019.01329>

⚠️ Do not forget to cite which version you used:
<https://doi.org/10.5281/zenodo.5797920>

### Others

- NPClassifier: <https://doi.org/10.1021/acs.jnatprod.1c00399>

## Additional software credits

```{r}
#| echo: false
#| message: false

# Check if DESCRIPTION is in current dir
# Else `altdoc` will not find the dependencies
desc_path <- if (file.exists("DESCRIPTION")) {
  "."
} else {
  ".."
}
grateful::cite_packages(
  output = "table",
  out.dir = getwd(),
  path = desc_path
) |>
  knitr::kable()
```