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Update readme and other repo MD files (#1063)
* Update readme * Move roadmap to main docs site * Avoid duplication by just putting a pointer to the actual docs
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| # contributing to cellxgene | ||
| We warmly welcome contributions from the community! | ||
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| We warmly welcome contributions from the community! Please submit any bug reports and feature requests through [Github issues](https://github.com/chanzuckerberg/cellxgene/issues). Please submit any direct contributions by forking the repository, creating a branch, and submitting a Pull Request. It'd be great for PRs to include test cases and documentation updates where relevant, though we know the core test suite is itself still a work in progress. | ||
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| All code contributions and dependencies must be compatible with the project's [open-source license (MIT)](LICENSE.txt). | ||
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| This project adheres to the Contributor Covenant | ||
| [code of conduct](https://github.com/chanzuckerberg/.github/tree/master/CODE_OF_CONDUCT.md). | ||
| By participating, you are expected to uphold this code. Please report unacceptable behavior | ||
| to [email protected]. | ||
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| And finally, if you have any questions about any of this stuff, just ask! :) | ||
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| ## developer guide | ||
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| This project has made a few key design choices | ||
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| - The front-end is built with [`regl`](https://github.com/regl-project/regl) (a webgl library), [`react`](https://reactjs.org/), [`redux`](https://redux.js.org/), [`d3`](https://github.com/d3/d3), and [`blueprint`](https://blueprintjs.com/docs/#core) to handle rendering large numbers of cells with lots of complex interactivity | ||
| - The app is designed with a client-server model that can support a range of existing analysis packages for backend computational tasks (currently built for [scanpy](https://github.com/theislab/scanpy)) | ||
| - The client uses fast cross-filtering to handle selections and comparisons across subsets of data | ||
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| Depending on your background and interests, you might want to contribute to the frontend, or backend, or both! | ||
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| If you are interested in working on `cellxgene` development, we recommend cloning the project from Gitub. First you'll need the following installed on your machine | ||
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| - python 3.6+ | ||
| - node and npm (we recommend using [nvm](https://github.com/creationix/nvm) if this is your first time with node) | ||
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| Then clone the project | ||
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| ``` | ||
| git clone https://github.com/chanzuckerberg/cellxgene.git | ||
| ``` | ||
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| Build the client web assets by calling `make` from inside the `cellxgene` folder | ||
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| ``` | ||
| make | ||
| ``` | ||
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| Install all requirements (we recommend doing this inside a virtual environment) | ||
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| ``` | ||
| pip install -e . | ||
| ``` | ||
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| You can start the app while developing either by calling `cellxgene` or by calling `python -m server`. We recommend using the `--debug` flag to see more output, which you can include when reporting bugs. | ||
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| If you have any questions about developing or contributing, come hang out with us by joining the [CZI Science Slack](https://join-cellxgene-users.herokuapp.com/) and posting in the `#cellxgene-dev` channel. | ||
| Whether you want to contribute ideas, requests, documentation, or code, you can get started by visiting our [contribution guide](https://chanzuckerberg.github.io/cellxgene/posts/contribute). |
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| <img src="./docs/cellxgene-logo.svg" width="300"> | ||
| <img src="./docs/cellxgene-logo.png" width="300"> | ||
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| _an interactive explorer for single-cell transcriptomics data_ | ||
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| [](https://zenodo.org/badge/latestdoi/105615409) [](https://pypi.org/project/cellxgene/) [](https://pypistats.org/packages/cellxgene) [](https://github.com/chanzuckerberg/cellxgene/pulse) | ||
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| cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the [Human Cell Atlas](https://humancellatlas.org). Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data. | ||
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| <img src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-demo-1.gif" width="200" height="200" hspace="30"><img src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-demo-2.gif" width="200" height="200" hspace="30"><img src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-demo-3.gif" width="200" height="200" hspace="30"> | ||
| Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data. | ||
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| - Want to install and use cellxgene? Visit the [cellxgene docs](https://chanzuckerberg.github.io/cellxgene/). | ||
| - Want to see where we are going? Check out [our roadmap](https://github.com/chanzuckerberg/cellxgene/blob/master/ROADMAP.md). | ||
| - Want to contribute? See our [contributors guide](https://github.com/chanzuckerberg/cellxgene/blob/master/CONTRIBUTING.md). | ||
| <img src="https://github.com/chanzuckerberg/cellxgene/raw/master/docs/images/crossfilter.gif" width="350" height="200" hspace="30"><img src="https://github.com/chanzuckerberg/cellxgene/raw/master/docs/images/category-breakdown.gif" width="350" height="200" hspace="30"> | ||
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| ## quick start | ||
| # Getting started | ||
| ### The comprehensive guide to cellxgene | ||
| [The cellxgene documentation is your one-stop-shop for information about cellxgene](https://chanzuckerberg.github.io/cellxgene/)! You may be particularly interested in: | ||
| * Seeing [what cellxgene can do](https://chanzuckerberg.github.io/cellxgene/posts/gallery) | ||
| * Learning more about cellxgene [installation](https://chanzuckerberg.github.io/cellxgene/posts/install) and [usage](https://chanzuckerberg.github.io/cellxgene/posts/launch) | ||
| * [Preparing your own data](https://chanzuckerberg.github.io/cellxgene/posts/prepare) for use in cellxgene | ||
| * Checking out [our roadmap](https://chanzuckerberg.github.io/cellxgene/posts/roadmap) for future development | ||
| * [Contributing](https://chanzuckerberg.github.io/cellxgene/posts/contribute) to cellxgene | ||
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| To install cellxgene you need Python 3.6+. We recommend [installing cellxgene into a conda or virtual environment.](https://chanzuckerberg.github.io/cellxgene/faq.html#how-do-i-create-a-python-36-environment-for-cellxgene) | ||
| ### Quick start | ||
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| Install the package. | ||
| To install cellxgene you need Python 3.6+. We recommend [installing cellxgene into a conda or virtual environment.](https://chanzuckerberg.github.io/cellxgene/posts/install) | ||
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| ```bash | ||
| Install the package. | ||
| ``` bash | ||
| pip install cellxgene | ||
| ``` | ||
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| Download an example [anndata](https://anndata.readthedocs.io/en/latest/) file | ||
| Launch cellxgene with an example [anndata](https://anndata.readthedocs.io/en/latest/) file | ||
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| ```bash | ||
| curl -O https://cellxgene-example-data.czi.technology/pbmc3k.h5ad.zip | ||
| unzip pbmc3k.h5ad | ||
| ``` bash | ||
| cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad | ||
| ``` | ||
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| Launch cellxgene | ||
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| ```bash | ||
| cellxgene launch pbmc3k.h5ad --open | ||
| ``` | ||
| To explore more datasets already formatted for cellxgene, check out the [Demo data](https://chanzuckerberg.github.io/cellxgene/posts/demo-data) or | ||
| see [Preparing your data](https://chanzuckerberg.github.io/cellxgene/posts/prepare) to learn more about formatting your own | ||
| data for cellxgene. | ||
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| To learn more about what you can do with cellxgene, see the [Getting Started](https://chanzuckerberg.github.io/cellxgene/getting-started.html) guide. | ||
| ### Finding help | ||
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| ## get in touch | ||
| We'd love to hear from you! | ||
| For questions, suggestions, or accolades, [join the `#cellxgene-users` channel on the CZI Science Slack](https://join-cellxgene-users.herokuapp.com/) and say "hi!". | ||
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| Have questions, suggestions, or comments? You can come hang out with us by joining the [CZI Science Slack](https://join-cellxgene-users.herokuapp.com/) and posting in the `#cellxgene-users` channel. Have feature requests or bugs? Please submit these as [Github issues](https://github.com/chanzuckerberg/cellxgene/issues). We'd love to hear from you! | ||
| For any errors, [report bugs on Github](https://github.com/chanzuckerberg/cellxgene/issues). | ||
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| ## contributing | ||
| # Developing with cellxgene | ||
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| We warmly welcome contributions from the community! Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene/blob/master/CONTRIBUTING.md) and don't hesitate to open an issue or send a pull request to improve cellxgene. | ||
| ### Contributing | ||
| We warmly welcome contributions from the community! Please see our [contributing guide](https://chanzuckerberg.github.io/cellxgene/posts/contribute) and don't hesitate to open an issue or send a pull request to improve cellxgene. | ||
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| This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/master/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [email protected]. | ||
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| ## core team | ||
| ### Reuse | ||
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| This project was started with the sole goal of empowering the scientific community to explore and understand their data. As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from this project, and reach out to us with ideas or questions. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT). | ||
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| ### Security | ||
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| If you believe you have found a security issue, we would appreciate notification. Please send email to <[email protected]>. | ||
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| # About | ||
| ### Core team | ||
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| The current core team: | ||
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@@ -61,21 +75,7 @@ We would also like to gratefully acknowledge contributions from past core team m | |
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| - Charlotte Weaver, software engineer | ||
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| ## where we are going | ||
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| Our goal is to enable teams of computational and experimental | ||
| biologists to collaboratively gain insight into their single-cell RNA-seq data. | ||
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| There are 4 key features we plan to implement in the near term. | ||
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| - Click install and launch | ||
| - Manual annotation workflows | ||
| - Toggle embeddings | ||
| - Gene information | ||
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| For more detail on these features and where we are going, see [our roadmap](https://github.com/chanzuckerberg/cellxgene/blob/master/ROADMAP.md). | ||
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| ## inspiration | ||
| ### Inspiration | ||
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| We've been heavily inspired by several other related single-cell visualization projects, including the [UCSC Cell Browswer](http://cells.ucsc.edu/), [Cytoscape](http://www.cytoscape.org/), [Xena](https://xena.ucsc.edu/), [ASAP](https://asap.epfl.ch/), [Gene Pattern](http://genepattern-notebook.org/), and many others. We hope to explore collaborations where useful as this community works together on improving interactive visualization for single-cell data. | ||
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| We have been working closely with the [scanpy](https://github.com/theislab/scanpy) team to integrate with their awesome analysis tools. Special thanks to Alex Wolf, Fabian Theis, and the rest of the team for their help during development and for providing an example dataset. | ||
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| We are eager to explore integrations with other computational backends such as [Seurat](https://github.com/satijalab/seurat) or [Bioconductor](https://github.com/Bioconductor) | ||
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| ## reuse | ||
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| This project was started with the sole goal of empowering the scientific community to explore and understand their data. As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from this project, and reach out to us with ideas or questions. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT). | ||
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| ## security | ||
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| If you believe you have found a security issue, we would appreciate notification. Please send email to <[email protected]>. | ||
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