XLRanker

XLRanker is a tool to rank and prioritize protein to protein cross linking data. The tool uses parsimonious selection as well as an XGBoost model to select the best protein pairs to represent ambiguous peptides.

Installation

You can install xlranker using pip:

pip install xlranker

Usage

While optional, it is recommended to create a config file to customize all of your parameters. The init command will create interactive prompts to create your custom config file.

xlranker init

To analyze a TSV file containing a network of peptide sequences with omics data,

xlranker start -n peptide_network.tsv -d omic_data/

or if you have created a config (strongly recommended), you can run

xlranker start -c config.yaml

Please view the documentation for detailed usage instructions and examples.

Example Notebook

For a quick start, you can check out the example notebook in the notebooks directory or launch a google colab notebook to see how to use the package interactively.