{
    "info": {
        "author": "Catherine Rawlinson",
        "author_email": "catherine.rawlinson@curtin.edu.au",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: Apache Software License",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7"
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        "description": "# BioDendro\n\n**A package to cluster metabolomics data, and plot dendrograms**\n\n[![Build Status](https://travis-ci.org/ccdmb/BioDendro.svg?branch=master)](https://travis-ci.org/ccdmb/BioDendro)\n\n## Background\n\n- Project owner: Catherine Rawlinson (PhD candidate)\n- Email: catherine.rawlinson@postgrad.curtin.edu.au\n\nConverts MGF format and component list into non-redundant list.\nComponent-analyte list is converted into a data matrix and analytes are dynamically binned and clustered.\n\n## Install on Linux or Mac from bash\n\nInstalling is easiest with pip.\nAssuming you have python3 installed you can run the following to install.\n\n```bash\npython3 -m pip install --user biodendro\n\n# or\n\ngit clone git@github.com:CurtinIC/BioDendro.git && cd BioDendro\npython3 -m pip install --user biodendro\n```\n\nThe `--user` flag tells pip to install to a user directory rather than a system directory.\nGenerally this will be under `~/.local` for Mac and Linux.\nMake sure that `~/.local/bin` is added to your `$PATH` if this is the case [see here](https://stackoverflow.com/questions/14637979/how-to-permanently-set-path-on-linux-unix).\n\nFor more advanced users, we recommend using a [virtual environment](https://virtualenv.pypa.io/en/stable/) or [conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).\n\nTo install as root, you can omit `--user`, though this is generally discouraged.\n\n```bash\nsudo python3 -m pip install biodendro\n```\n\nTo install the latest and greatest version, you can use [git](https://git-scm.com/), to install directly from the repository.\n\n```bash\npython3 -m pip install --user git+https://github.com/CurtinIC/BioDendro.git\n\n# or\n\ngit clone git@github.com:CurtinIC/BioDendro.git && cd BioDendro\npython3 -m pip install --user .\n```\n\nBoth the `BioDendro` script and the python package will now be available to use (assuming Python is configured correctly).\n\n\n## Quick Start Example - command line\n\nThe quickest way to run is using the command-line interface.\n\nA list of options can be obtained with the `--help` flag.\n\n```bash\nBioDendro --help\n```\n\nTo run the basic pipeline using the example MGF and components file do:\n\n```bash\nBioDendro --results-dir my_results_dir MSMS.mgf component_list.txt\n```\n\n\n## Quick Start Example - Python library\n\nThe pipeline is also available as a python function/library.\nThe command above would be equivalent to the following in python.\n\n```python\nimport BioDendro\n\ntree = BioDendro.pipeline(\"MSMS.mgf\", \"component_list.txt\", results_dir=\"my_results_dir\")\n```\n\nFrom there you could analyse the results stored in `tree`.\nThe example jupyter notebooks contain more detailed explanations of different parameters.\n\n[quick-start-example.ipynb](quick-start-example.ipynb) contains basic information about running the pipelines.\n\n[longer-example.ipynb](longer-example.ipynb) contains more detailed information about how the pipeline works, and how you can modify parameters.\n\n\n![Scheme](cluster-d10.png \"Clustering\")\n\n\n## Command line API\n\nThe pipeline can also be run from a bash or bash-like terminal.\nThis is useful if you're not planning on tweaking the parameters much and just want to run the darn thing.\n\nFor these examples, we're using the ipython magic command `%%bash` to run the commands in bash.\nYou can omit the %%bash bit if you're running straight in the terminal.\n\nTo get a list of all options available use the `--help` (or `-h`) flag.\n\n```bash\n%%bash\nBioDendro --help\n```\nThe minimum options to run the pipeline are the MGF file and a components list.\n\nUsing the example data in the BioDendro repo we could run...\n\n```bash\n%%bash\n\nBioDendro MSMS.mgf component_list.txt\n```\n\nAs before, the results will be stored in a directory with the current date and the current time added to the end of it.\n\nYou can change the parameters to use by supplying additional flags, however, this will run the whole pipeline again, so it you just need to adjust the cutoff or decide to use braycurtis instead of jaccard distances, you might be better off using the python API.\n\n```bash\n%%bash\n\nBioDendro --scaling --cluster-method braycurtis --cutoff 0.5 MSMS.mgf component_list.txt\n```\n\nwould be equivalent to running the following in python\n\n```python\ntree = BioDendro.pipeline(\"MSMS.mgf\", \"component_list.txt\", clustering_method=\"braycurtis\", scaling=True, cutoff=0.5)\n```",
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