Progress Report: Genome-wide hypothesis generation for single-cell expression via latent spaces of deep neural networks

Manuscript description

We wrote an application for the Chan Zuckerberg Initiative's Collaborative Computational Tools RFA. Our application was recommended for funding. We are writing our progress report as we go. This repository contains the report. Please feel free to file a GitHub Issue to ask a question. Some elements of this report are expected to also be written up via a published manuscript. In the event that we write a manuscript, we will begin from this report. Authorship will be determined in accordance with ICMJE guidelines.

Manubot

Manubot is a system for writing scholarly manuscripts via GitHub. Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub. The Manubot Rootstock repository is a general purpose template for creating new Manubot instances, as detailed in SETUP.md. See USAGE.md for documentation how to write a manuscript.

Please open an issue for questions related to Manubot usage, bug reports, or general inquiries.

Repository directories & files

The directories are as follows:

• content contains the manuscript source, which includes markdown files as well as inputs for citations and references. See USAGE.md for more information.
• output contains the outputs (generated files) from the manubot including the resulting manuscripts. You should not edit these files manually, because they will get overwritten.
• webpage is a directory meant to be rendered as a static webpage for viewing the HTML manuscript.
• build contains commands and tools for building the manuscript.
• ci contains files necessary for deployment via continuous integration. For the CI configuration, see .travis.yml.

Local execution

To run the Manubot locally, install the conda environment as described in build. Then, you can build the manuscript on POSIX systems by running the following commands.

# Activate the manubot conda environment (assumes conda version >= 4.4)
conda activate manubot

# Build the manuscript
sh build/build.sh

# Or monitor the content directory, and automatically rebuild the manuscript
# when a change is detected.
sh build/autobuild.sh

# View the manuscript locally at http://localhost:8000/
cd webpage
python -m http.server

Continuous Integration

Whenever a pull request is opened, Travis CI will test whether the changes break the build process to generate a formatted manuscript. The build process aims to detect common errors, such as invalid citations. If your pull request build fails, see the Travis CI logs for the cause of failure and revise your pull request accordingly.

When a commit to the master branch occurs (for example, when a pull request is merged), Travis CI builds the manuscript and writes the results to the gh-pages and output branches. The gh-pages branch uses GitHub Pages to host the following URLs:

• HTML manuscript at https://greenelab.github.io/czi-hca-report/
• PDF manuscript at https://greenelab.github.io/czi-hca-report/manuscript.pdf

For continuous integration configuration details, see .travis.yml.

License

Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License (LICENSE.md), which allows reuse with attribution. Please attribute by linking to https://github.com/greenelab/czi-hca-report.

Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (LICENSE-CC0.md). All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:

• *.sh
• *.py
• *.yml / *.yaml
• *.json
• *.bib
• *.tsv
• .gitignore

All other files are only available under CC BY 4.0, including:

• *.md
• *.html
• *.pdf
• *.docx

Except for the following files with different licenses:

• build/assets/anchors.js which is released under an MIT License

Please open an issue for any question related to licensing.