{"id":20074748,"url":"https://github.com/greenelab/netscape","last_synced_at":"2026-05-09T21:45:14.676Z","repository":{"id":77738012,"uuid":"196423475","full_name":"greenelab/netscape","owner":"greenelab","description":"Exploring the network/pathway regularization landscape for gene expression data","archived":false,"fork":false,"pushed_at":"2020-02-25T21:54:32.000Z","size":6382,"stargazers_count":0,"open_issues_count":4,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-13T00:41:45.058Z","etag":null,"topics":["analysis","gene-expression","methodology","networks","pathways","tool"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/greenelab.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-07-11T15:45:09.000Z","updated_at":"2020-09-29T20:27:11.000Z","dependencies_parsed_at":"2023-03-12T01:52:57.771Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/netscape","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fnetscape","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fnetscape/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fnetscape/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fnetscape/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/netscape/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241506338,"owners_count":19973586,"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":["analysis","gene-expression","methodology","networks","pathways","tool"],"created_at":"2024-11-13T14:54:09.551Z","updated_at":"2026-05-09T21:45:14.642Z","avatar_url":"https://github.com/greenelab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# netscape\n\nExploring the **net**work/pathway regularization land**scape** for gene expression data\n\nOverall goal of this project: evaluate network regularized methods for\na variety of practical problems using a variety of biological networks.\n\nAt present, this repo contains an adaptation of the pipeline used in\n[BioBombe](https://github.com/greenelab/BioBombe) for predicting gene\nalteration status using TCGA gene expression data.\n\n## Setup\n\nWe recommend using the conda environment specified in the `environment.yml` file to run these analyses. To build and activate this environment, run:\n\n```shell\n# conda version 4.5.0\nconda env create --file environment.yml\n\nconda activate netreg\n```\n\nTo run PLIER, you'll have to install it from GitHub using the\n`devtools` library. Run the following from an R interactive shell/\nREPL inside the `netreg` Conda environment:\n\n```R\nlibrary(devtools)\ninstall_github('wgmao/PLIER')\n\n```\n\nYou should then be able to run the `library(PLIER)` command\nwithout errors.\n\n## Running tests\n\nRunning the tests requires the `pytest` module (included in the specified\nConda environment). Once this module is installed, you can run the tests\nby executing the command\n\n```shell\npytest tests/\n```\n\nfrom the repo root.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fnetscape","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fnetscape","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fnetscape/lists"}