{"id":20074663,"url":"https://github.com/greenelab/stanmf","last_synced_at":"2025-05-05T21:32:04.290Z","repository":{"id":57471052,"uuid":"64495915","full_name":"greenelab/staNMF","owner":"greenelab","description":"A python implementation of Stability NMF","archived":false,"fork":false,"pushed_at":"2016-11-23T18:58:18.000Z","size":5351,"stargazers_count":6,"open_issues_count":3,"forks_count":3,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-08-09T02:17:01.331Z","etag":null,"topics":["analysis","gene-expression","machine-learning","tool"],"latest_commit_sha":null,"homepage":"","language":"Python","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.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-07-29T16:44:52.000Z","updated_at":"2020-10-27T19:29:13.000Z","dependencies_parsed_at":"2022-09-10T10:51:19.150Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/staNMF","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%2FstaNMF","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2FstaNMF/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2FstaNMF/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2FstaNMF/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/staNMF/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224470634,"owners_count":17316704,"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","machine-learning","tool"],"created_at":"2024-11-13T14:53:19.132Z","updated_at":"2024-11-13T14:53:19.811Z","avatar_url":"https://github.com/greenelab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Amy Campbell, 2016\n\n\nstaNMF\n------\nPython 2.7 implementation of `Siqi Wu et al.'s 2016 stability NMF (staNMF)\n\u003chttp://doi.org/10.1073/pnas.1521171113\u003e`_\n\nPackage Contents\n----------------\n\n=========\nstaNMF.py\n=========\nstaNMF.py class includes the necessary methods to perform stability\nNMF on a user-specified .csv datase (see sourcecode/staNMF_Example for precise\nusage instructions)\n\n=================\nstaNMF_Example.py\n=================\nExample of staNMF demonstrated on Wu et al.'s 2016\ndrosophila spatial expression data between K=15 and K=30; Generates\nsample factorizations, calculates instability index, and plots instability\nagainst K\n\n================\nstaNMF_driver.py\n================\nDriver script to run staNMF in parallel; can be called from the command line\nusing:\npython staNMF_driver.py \u003ck1\u003e \u003ck2\u003e \u003creps1\u003e \u003creps2\u003e \u003cfolder\u003e \u003cfilename\u003e \u003cfunction\u003e\n(See docstring for more specific instructions) \n\n============================\ndata/WuExampleExpression.csv\n============================\nsample dataset (also available for download `here\n\u003chttp://insitu.fruitfly.org/cgi-bin/ex/insitu.pl?t=html\u0026p=downloads\u003e`_)\n\n\nInstallation\n-------------\n$ pip install staNMF\n\n*Please note that staNMF requires SPAMs package (version 2.5), which is\navailable from* `Julien Mairal et al.\n\u003chttp://spams-devel.gforge.inria.fr/downloads.html\u003e`_ , or from Anaconda\nusing:\n\n$ conda install -c conda-forge python-spams=2.5\n\n\nAcknowledgements\n----------------\nThis work was supported by The Gordon and Betty Moore Foundation’s Data-Driven\nDiscovery Initiative (GBMF 4552 to C.S.G.) and a grant from the National\nInstitutes of Health (R01 CA200854)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fstanmf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fstanmf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fstanmf/lists"}