Installation improvements and new README

.gitignore

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+# Project-specific data directories
+inputs/
+output/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

README.md

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-# ReducingVariantClassificationInequities
+# Analysis Notebooks for Reducing Variant Classification Inequalities
+
+This repository contains the [Jupyter notebook](https://jupyter.org/) used to generate figures and key results for
+"Defining and Reducing Variant Classification Inequities in Genomic Medicine" by Dawood ... Gallego Romero 
+(final citation TBA).
+
+## How to use this notebook
+
+### Getting set up
+
+To begin, 
+[clone the repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
+so that you have a local copy of the notebook and the required directory structure.
+
+Create a [new virtual Python environment](https://docs.python.org/3/library/venv.html) for running the notebooks.
+The notebooks have been tested using Python 3.7 and Python 3.10, but other versions are likely to work as well.
+Activate the environment and install the required packages defined in `requirements.txt`.
+
+The following commands will set up and launch the notebook on a Unix-like system:
+
+```
+git clone git@github.com:MoezDawood/ReducingVariantClassificationInequities.git
+cd ReducingVariantClassificationInequities
+python3 -m venv env
+source env/bin/activate
+pip install -r requirements.txt
+jupyter notebook ReducingVariantClassificationInequitiesCode_20240311.ipynb
+```
+
+### Downloading required data files
+
+Running the notebook requires several large collections of variants from [gnomAD](https://gnomad.broadinstitute.org/)
+and other sources.
+Pre-formatted files can be downloaded from 
+[this link](https://drive.google.com/drive/folders/1cdXoB0AMPCO0dWH_6Eff1smtCd5i5YPB?usp=drive_link)
+and extracted into the `inputs/` folder in the same directory as the notebook file.
+
+### Reproducing the results
+
+It will take around 5-6 hours to produce all figures and tables found in the paper
+(including main text figures and supplement and a few additional figures) for gnomAD v2.1.1 and gnomAD v3.1.2 (non v2).
+The figures and tables will be found in the output folder.
+
+The notebook is designed to be run from start to finish, 
+but there is a table of contents and users should be able to reproduce individual figures once the setup is completed.
+
+Note that due to the large size of the data frames containing all the required variant information,
+running this notebook requires a computer with a large amount of memory and we recommend using a shared server or cluster node for this purpose.
+
+### Data and code availability for All of Us
+
+Per the policy of the All of Us program, the code, inputs, and outputs for the All of Us analyses is in a declared workspace in the All of Us workbench.
+The code in the All of Us workspace is the same as below with modifications made for the specific data requirements of the All of Us platform.
+The workspace will be gladly and immediately shared with approved users upon request.