{"id":21287738,"url":"https://github.com/stjudecloud/expression-classification","last_synced_at":"2025-07-26T11:39:13.032Z","repository":{"id":39900792,"uuid":"226388270","full_name":"stjudecloud/expression-classification","owner":"stjudecloud","description":null,"archived":false,"fork":false,"pushed_at":"2025-04-11T15:03:21.000Z","size":495,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-07-11T14:27:22.320Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/stjudecloud.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.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,"zenodo":null}},"created_at":"2019-12-06T18:36:24.000Z","updated_at":"2025-04-11T15:03:26.000Z","dependencies_parsed_at":"2024-04-16T14:38:27.393Z","dependency_job_id":"d23e70b4-9e86-47d9-8c59-d03ebbde25e5","html_url":"https://github.com/stjudecloud/expression-classification","commit_stats":null,"previous_names":[],"tags_count":22,"template":false,"template_full_name":null,"purl":"pkg:github/stjudecloud/expression-classification","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fexpression-classification","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fexpression-classification/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fexpression-classification/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fexpression-classification/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stjudecloud","download_url":"https://codeload.github.com/stjudecloud/expression-classification/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fexpression-classification/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267161367,"owners_count":24045473,"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","status":"online","status_checked_at":"2025-07-26T02:00:08.937Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2024-11-21T12:15:34.116Z","updated_at":"2025-07-26T11:39:13.007Z","avatar_url":"https://github.com/stjudecloud.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Interactive t-SNE\n\nCode used to generate interactive t-SNE plots using RNA-Seq counts data.\n\n## Getting Started\n\nThese instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.\n\n### Prerequisites\n\nTo get started, you'll want to have Python 3 and R 3.6.1.\n\n```bash\nconda create -n itsne-dev \\\n             -c conda-forge \\\n             -c bioconda \\\n             r-base=3.6.1 \\\n             python=3.7 \\\n             logzero \\\n             numpy \\\n             pandas \\\n             scikit-learn \\\n             bioconductor-biocinstaller \\\n             bioconductor-sva \\\n             bioconductor-deseq2 \\\n             r-tsne r-getopt r-plotly r-optparse r-rtsne r-pracma r-data.table -y\nconda activate itsne-dev\n```\n\nAlternatively, you can install the anaconda dependencies directly from the `environment.yml` file.\n\n```bash\nconda env create -f environment.yml\n```\n\n### Installing\n\nFirst, the author recommends you run the following command line script to ensure all R\npackages are loaded before your first run:\n\n```bash\nRscript scripts/itsne-normalize-matrix.R\n```\n\nFrom here, you can install the python package:\n\n```bash\npython3 setup.py install\n```\n\nDownload the relevant gene model:\n\n```bash\ncurl ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/gencode.v31.annotation.gtf.gz -o gencode.v31.annotation.gtf.gz\n```\n\nAnd try out the script:\n\n```bash\nitsne-main counts/* \\\n           -b reference/gene.excludelist.tsv \\\n           -c reference/covariates.tsv \\\n           -g gencode.v31.annotation.gtf.gz \\\n           -o tsne.html\n```\n\n## Running the tests\n\nNo tests currently exist. If and when tests are added, the authors will fill in this section.\n\n## Contributing\n\nPlease read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.\n\n## Versioning\n\nWe use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/stjudecloud/expression-classification/tags). \n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Fexpression-classification","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstjudecloud%2Fexpression-classification","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Fexpression-classification/lists"}