{"id":21274993,"url":"https://github.com/maayanlab/scavi","last_synced_at":"2025-07-11T07:30:33.755Z","repository":{"id":42359462,"uuid":"138074504","full_name":"MaayanLab/scAVI","owner":"MaayanLab","description":"Single-cell RNA-seq data analysis and visualization","archived":false,"fork":false,"pushed_at":"2022-12-02T13:02:00.000Z","size":15957,"stargazers_count":4,"open_issues_count":22,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2023-03-31T16:29:45.877Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://amp.pharm.mssm.edu/scavi","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MaayanLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-06-20T19:03:12.000Z","updated_at":"2022-06-12T20:57:06.000Z","dependencies_parsed_at":"2023-01-23T00:30:14.155Z","dependency_job_id":null,"html_url":"https://github.com/MaayanLab/scAVI","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FscAVI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FscAVI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FscAVI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FscAVI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MaayanLab","download_url":"https://codeload.github.com/MaayanLab/scAVI/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225703744,"owners_count":17510960,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":"2024-11-21T09:26:43.595Z","updated_at":"2024-11-21T09:26:44.723Z","avatar_url":"https://github.com/MaayanLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# scAVI\nscAVI is a web-based platform developed to enable users to analyze and visualize published and not published single cell RNA sequencing (scRNA-seq) datasets with state-of-the-art algorithms and visualization methods.\n\nThe scAVI platform supports the analysis and visualization of 463 publicly available scRNA-seq studies from GEO covering 194,653 single cells/samples. Analyses are provided as 463 dedicated landing pages and Jupyter Notebook reports for each study.\n\n## Deploying\n\n### Environment\nscAVI depends on several external elements including:\n- biojupies notebook generator\n  - google cloud storage of notebooks\n  - mysql for registration of notebooks\n- scavi visualization\n  - mongodb for pca/coords \u0026 metadata\n\nThe `Dockerfile` has detailed directions about setting up a system with the necessary R \u0026 python dependencies while the `docker-compose.yml` demonstrates how scavi can connect to the various external components. More likely, you would run those databases on the cloud and configure them.\n\nThe `.env.example` file has some example values, it can be copied over to `.env` and modified with the credentials and paths you use in your own application prior to using the docker-compose.\n\nFor help setting up scavi for yourself it is recommended that you contact us for further direction.\n\n### NPM\nWe use nodejs for some of the UI development, for this purpose the npm package manager has a `package.json` file which identifies all necessary dependencies. Assuming you already have npm installed, this is a simple `npm install` command. For more information on npm, including installing it, please consult the [npm docs](https://docs.npmjs.com/).\n\n### Docker\nWe use `Dockerfile` and `docker-compose.yml` to document the process of constructing a complete virtual system capable of running this application. This includes R and python installations; the docker-compose goes a level higher and documents how scavi interacts with external databases. For more information on using docker-compose, please consult the [docker-compose documentation](https://docs.docker.com/compose/)..\n\n```bash\n# Ensure you install npm dependencies in the static directory prior to building the dockerfile\ncd static \u0026\u0026 npm i\n# Then build the dockerfile\ndocker-compose build scavi\n# And run\ndocker-compose up scavi\n# Or deploy\ndocker-compose push scavi\n```\n\n## Development\n\n### Installation\n#### Python2\n```bash\n# ensure virtualenv is installed\npython2 -m pip install virtualenv\n# ensure setup virtualenv\npython2 -m virtualenv venv\n# establish virtualenv\nsource venv/bin/activate\n# install packages\npip install -r requirements.txt\n```\n\n#### R\n```bash\n# ensure R stores things here\nexport R_LIBS=$(pwd)/renv\n# setup R environment\nR -e \"source('setup.R')\"\n```\n\n#### NodeJS\n```bash\ncd static\n# Install node dependencies\nnpm i\n```\n\n### Running in development\n```bash\n# activate environments\nsource venv/bin/activate\nexport R_LIBS=$(pwd)/renv\n# export .env variables\nset -o allexport\nsource .env\nset +o allexport\n# run\nbash run.sh\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fscavi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaayanlab%2Fscavi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fscavi/lists"}