{"id":43499309,"url":"https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot","last_synced_at":"2026-02-03T11:13:24.887Z","repository":{"id":247445565,"uuid":"825868018","full_name":"xomicsdatascience/transcriptome-proteome-nas-manubot","owner":"xomicsdatascience","description":null,"archived":false,"fork":false,"pushed_at":"2024-11-11T23:54:04.000Z","size":6363,"stargazers_count":5,"open_issues_count":5,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-11-12T00:32:09.653Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/xomicsdatascience.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE-CC0.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-07-08T16:52:57.000Z","updated_at":"2024-10-27T22:08:50.000Z","dependencies_parsed_at":"2024-11-12T00:26:30.396Z","dependency_job_id":"06d9f689-677e-4c18-9cda-92aca8a6a4c7","html_url":"https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot","commit_stats":null,"previous_names":["xomicsdatascience/transcriptome-proteome-nas-manubot"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/xomicsdatascience/transcriptome-proteome-nas-manubot","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Ftranscriptome-proteome-nas-manubot","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Ftranscriptome-proteome-nas-manubot/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Ftranscriptome-proteome-nas-manubot/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Ftranscriptome-proteome-nas-manubot/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xomicsdatascience","download_url":"https://codeload.github.com/xomicsdatascience/transcriptome-proteome-nas-manubot/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Ftranscriptome-proteome-nas-manubot/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29044101,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T10:09:22.136Z","status":"ssl_error","status_checked_at":"2026-02-03T10:09:16.814Z","response_time":96,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-02-03T11:13:24.069Z","updated_at":"2026-02-03T11:13:24.880Z","avatar_url":"https://github.com/xomicsdatascience.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Multi-Omic Integration with Deep Learning\n\n\u003c!-- usage note: edit the H1 title above to personalize the manuscript --\u003e\n\n[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://xomicsdatascience.github.io/transcriptome-proteome-nas-manubot/)\n[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://xomicsdatascience.github.io/transcriptome-proteome-nas-manubot/manuscript.pdf)\n[![GitHub Actions Status](https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot/workflows/Manubot/badge.svg)](https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot/actions)\n\n## Manuscript description\n\n\u003c!-- usage note: edit this section. --\u003e\n\n### Collaboration Offer\n \nThis paper was a singular effort from the Meyer Lab at Cedars Sinai Medical Center in LA. The intent was to use deep learning methods to tease out possible transcript-protein relationships of biological significance in cancer data and, looking ahead, beyond. The paper establishes several directions we went in interpreting SHAP values to achieve this aim. However, we understand that SHAP values can provide greater insights than we specifically explored, and that other researchers would be interested in performing additional analyses. Thus, in addition to our preprint submission, we have created this manubot version of the paper.\n \nFor interested researchers, contributions to the paper would be tracked for inclusion as authors in the final submission. As an authorship requirement you must contribute at least one figure that appears in the paper, though that is open for discussion. To contribute, fork the repository, make your edits, then make a pull request. For data analysis, [CPTAC is freely available for use](https://github.com/PayneLab/cptac), and our [GitHub repository for our data analysis](https://github.com/xomicsdatascience/RnaToProteinDataModule) was written to be readable and reusable. In the data analysis repository, the original Neural Architectural Search is found in the main branch, and SHAP experimentation occurred in the input_residual_connections branch.\n \nPlease reach out via GitHub issues to discuss your proposed analysis and whether it would qualify for authorship.\n\n\n## Manubot\n\n\u003c!-- usage note: do not edit this section --\u003e\n\nManubot is a system for writing scholarly manuscripts via GitHub.\nManubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub.\nAn [overview manuscript](https://greenelab.github.io/meta-review/ \"Open collaborative writing with Manubot\") presents the benefits of collaborative writing with Manubot and its unique features.\nThe [rootstock repository](https://git.io/fhQH1) is a general purpose template for creating new Manubot instances, as detailed in [`SETUP.md`](SETUP.md).\nSee [`USAGE.md`](USAGE.md) for documentation how to write a manuscript.\n\nPlease open [an issue](https://git.io/fhQHM) for questions related to Manubot usage, bug reports, or general inquiries.\n\n### Repository directories \u0026 files\n\nThe directories are as follows:\n\n+ [`content`](content) contains the manuscript source, which includes markdown files as well as inputs for citations and references.\n  See [`USAGE.md`](USAGE.md) for more information.\n+ [`output`](output) contains the outputs (generated files) from Manubot including the resulting manuscripts.\n  You should not edit these files manually, because they will get overwritten.\n+ [`webpage`](webpage) is a directory meant to be rendered as a static webpage for viewing the HTML manuscript.\n+ [`build`](build) contains commands and tools for building the manuscript.\n+ [`ci`](ci) contains files necessary for deployment via continuous integration.\n\n### Local execution\n\nThe easiest way to run Manubot is to use [continuous integration](#continuous-integration) to rebuild the manuscript when the content changes.\nIf you want to build a Manubot manuscript locally, install the [conda](https://conda.io) environment as described in [`build`](build).\nThen, you can build the manuscript on POSIX systems by running the following commands from this root directory.\n\n```sh\n# Activate the manubot conda environment (assumes conda version \u003e= 4.4)\nconda activate manubot\n\n# Build the manuscript, saving outputs to the output directory\nbash build/build.sh\n\n# At this point, the HTML \u0026 PDF outputs will have been created. The remaining\n# commands are for serving the webpage to view the HTML manuscript locally.\n# This is required to view local images in the HTML output.\n\n# Configure the webpage directory\nmanubot webpage\n\n# You can now open the manuscript webpage/index.html in a web browser.\n# Alternatively, open a local webserver at http://localhost:8000/ with the\n# following commands.\ncd webpage\npython -m http.server\n```\n\nSometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected.\nThe following command, while running, will trigger both the `build.sh` script and `manubot webpage` command upon content changes:\n\n```sh\nbash build/autobuild.sh\n```\n\n### Continuous Integration\n\nWhenever a pull request is opened, CI (continuous integration) will test whether the changes break the build process to generate a formatted manuscript.\nThe build process aims to detect common errors, such as invalid citations.\nIf your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly.\n\nWhen a commit to the `main` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot/tree/gh-pages) and [`output`](https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot/tree/output) branches.\nThe `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs:\n\n+ **HTML manuscript** at https://xomicsdatascience.github.io/transcriptome-proteome-nas-manubot/\n+ **PDF manuscript** at https://xomicsdatascience.github.io/transcriptome-proteome-nas-manubot/manuscript.pdf\n\nFor continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml).\n\n## License\n\n\u003c!--\nusage note: edit this section to change the license of your manuscript or source code changes to this repository.\nWe encourage users to openly license their manuscripts, which is the default as specified below.\n--\u003e\n\n[![License: CC BY 4.0](https://img.shields.io/badge/License%20All-CC%20BY%204.0-lightgrey.svg)](http://creativecommons.org/licenses/by/4.0/)\n[![License: CC0 1.0](https://img.shields.io/badge/License%20Parts-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/)\n\nExcept when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License ([`LICENSE.md`](LICENSE.md)), which allows reuse with attribution.\nPlease attribute by linking to https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot.\n\nSince 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`](LICENSE-CC0.md)).\nAll files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:\n\n+ `*.sh`\n+ `*.py`\n+ `*.yml` / `*.yaml`\n+ `*.json`\n+ `*.bib`\n+ `*.tsv`\n+ `.gitignore`\n\nAll other files are only available under CC BY 4.0, including:\n\n+ `*.md`\n+ `*.html`\n+ `*.pdf`\n+ `*.docx`\n\nPlease open [an issue](https://github.com/xomicsdatascience/transcriptome-proteome-nas-manubot/issues) for any question related to licensing.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxomicsdatascience%2Ftranscriptome-proteome-nas-manubot","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fxomicsdatascience%2Ftranscriptome-proteome-nas-manubot","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxomicsdatascience%2Ftranscriptome-proteome-nas-manubot/lists"}