{"id":20074642,"url":"https://github.com/greenelab/pathcore-t","last_synced_at":"2025-05-05T21:31:57.069Z","repository":{"id":57451072,"uuid":"92404620","full_name":"greenelab/PathCORE-T","owner":"greenelab","description":"Methods to build a network of pathway co-occurrence relationships out of expression signatures extracted from transcriptomic compendia.","archived":false,"fork":false,"pushed_at":"2017-10-17T15:51:12.000Z","size":22,"stargazers_count":4,"open_issues_count":1,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-11-06T12:56:46.282Z","etag":null,"topics":["analysis","gene-expression","methodology","supplement"],"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","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-05-25T13:11:29.000Z","updated_at":"2020-10-27T19:30:29.000Z","dependencies_parsed_at":"2022-09-26T16:30:59.466Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/PathCORE-T","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2FPathCORE-T","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2FPathCORE-T/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2FPathCORE-T/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2FPathCORE-T/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/PathCORE-T/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224470625,"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","methodology","supplement"],"created_at":"2024-11-13T14:53:12.313Z","updated_at":"2024-11-13T14:53:12.978Z","avatar_url":"https://github.com/greenelab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"PathCORE-T\n----------\nPython 3 implementation of methods described in\n`Chen et al.'s 2017 PathCORE-T paper \u003chttps://doi.org/10.1101/147645\u003e`_.\n\nNote that this software was renamed from PathCORE to PathCORE-T in Oct 2017.\nThe T specifies that pathway co-occurrence relationships are identified using\nfeatures extracted from **transcriptomic** data. \nThe module itself is still named `pathcore` to maintain backwards\ncompatibility for users of the original PathCORE software package. \n\nThis code has been tested on Python 3.5.\nThe documentation for the modules in the package can be\n`accessed here \u003chttp://pathcore-demo.herokuapp.com/static/data/docs_pathcore/index.html\u003e`_.\n\nInstallation\n----------------\nTo install the current PyPI version (recommended), run::\n\n    pip install PathCORE-T\n\nFor the latest GitHub version, run::\n\n    pip install git+https://github.com/greenelab/PathCORE-T.git#egg=PathCORE-T\n\nExamples\n---------\nWe recommend that users of the PathCORE-T software begin by reviewing the\nexamples in the `PathCORE-T-analysis \u003chttps://github.com/greenelab/PathCORE-T-analysis\u003e`_\nrepository. The analysis repository contains shell scripts and wrapper\nanalysis scripts that demonstrate how to run the methods in this package\non features constructed from a broad compendium according to the \n`workflow we describe in our paper \u003chttps://github.com/greenelab/PathCORE-T-analysis#the-pathcore-analysis-workflow\u003e`_.\n\nSpecifically, `this Jupyter notebook \u003chttps://github.com/greenelab/PathCORE-T-analysis/blob/master/jupyter-notebooks/Supplemental_PAO1_FastICA_example.ipynb\u003e`_\nis a simple example of the workflow and a great place to start.\n\nPackage contents\n----------------\n\n=====================================\nfeature_pathway_overrepresentation.py\n=====================================\nThe methods in this module are used to identify the pathways\noverrepresented in features extracted from a transcriptomic dataset\nof genes-by-samples. Features must preserve the genes in the dataset\nand assign weights to these genes based on some distribution.\n[`feature_pathway_overrepresentation documentation. \u003chttp://pathcore-demo.herokuapp.com/static/data/docs_pathcore/source/pathcore.html#module-pathcore.feature_pathway_overrepresentation\u003e`_]\n\n===========\nnetwork.py\n===========\nContains the data structure ``CoNetwork`` that stores information\nabout the pathway co-occurrence network. The output from\na pathway enrichment analysis in ``feature_pathway_overrepresentation.py``\nserves as input into the ``CoNetwork`` constructor.\n[`CoNetwork documentation. \u003chttp://pathcore-demo.herokuapp.com/static/data/docs_pathcore/source/pathcore.html#module-pathcore.network\u003e`_]\n\n============================\nnetwork_permutation_test.py\n============================\nThe methods in this module are used to filter the constructed\nco-occurence network. We implement a permutation test that evaluates\nand removes edges (pathway-pathway relationships) in the network\nthat cannot be distinguished from a null model of random associations.\nThe null model is created by generating *N* permutations of the network.\n[`network_permutation_test documentation. \u003chttp://pathcore-demo.herokuapp.com/static/data/docs_pathcore/source/pathcore.html#module-pathcore.network_permutation_test\u003e`_]\n\nAcknowledgements\n----------------\nThis work was supported by the Penn Institute for Bioinformatics\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fpathcore-t","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fpathcore-t","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fpathcore-t/lists"}