{"id":16599961,"url":"https://github.com/dirmeier/rnaiutilities","last_synced_at":"2026-05-09T06:37:24.987Z","repository":{"id":133195933,"uuid":"179146359","full_name":"dirmeier/rnaiutilities","owner":"dirmeier","description":"A collection of python modules and command line tools for processing image-based RNAi screens.","archived":false,"fork":false,"pushed_at":"2019-04-02T21:35:09.000Z","size":58711,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-17T06:45:46.846Z","etag":null,"topics":["cellprofiler","database","microscopy","python","rnai","sqlite"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dirmeier.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"code-of-conduct.md","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":"2019-04-02T19:38:26.000Z","updated_at":"2020-05-19T18:10:52.000Z","dependencies_parsed_at":"2023-05-05T23:48:39.174Z","dependency_job_id":null,"html_url":"https://github.com/dirmeier/rnaiutilities","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/dirmeier%2Frnaiutilities","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dirmeier%2Frnaiutilities/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dirmeier%2Frnaiutilities/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dirmeier%2Frnaiutilities/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dirmeier","download_url":"https://codeload.github.com/dirmeier/rnaiutilities/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242538972,"owners_count":20145882,"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":["cellprofiler","database","microscopy","python","rnai","sqlite"],"created_at":"2024-10-12T00:13:08.493Z","updated_at":"2026-05-09T06:37:19.935Z","avatar_url":"https://github.com/dirmeier.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# rnaiutilities \u003cimg src=\"https://raw.githubusercontent.com/dirmeier/rnaiutilities/master/_fig/fig_single_cells.jpg\" align=\"right\" width=\"160px\"/\u003e\n\n[![Project Status](http://www.repostatus.org/badges/latest/inactive.svg)](http://www.repostatus.org/#inactive)\n[![Build](https://travis-ci.org/dirmeier/rnaiutilities.svg?branch=master)](https://travis-ci.org/dirmeier/rnaiutilities)\n[![Coverage](https://codecov.io/gh/dirmeier/rnaiutilities/branch/master/graph/badge.svg)](https://codecov.io/gh/dirmeier/rnaiutilities)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/451bb1a5b6bb46a499713f048f296ed4)](https://www.codacy.com/app/simon-dirmeier/rnaiutilities?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=dirmeier/rnaiutilities\u0026amp;utm_campaign=Badge_Grade)\n[![Documentation](https://readthedocs.org/projects/rnaiutilities/badge/?version=latest)](https://rnaiutilities.readthedocs.io/en/latest/?badge=latest)\n\n\nA collection of python modules and command line tools for processing image-based RNAi screens.\n\n## Introduction\n\n`rnaiutilities` provide a set of python modules and commandline scripts that can be used to process, convert, query and analyse imaged-based RNAi-screens.\n\nThe packages are designed for the following workflow:\n\n* Download raw `mat` files from an openBIS instance or where ever your data lie. The `mat` files are supposed to be created by `CellProfiler`, i.e. platewise data-sets, where every file describes a single features for single-cells.\n* Parse the downloaded data using `rnai-parse`: install the package, and process as described in the package folder. This generates a list of raw `tsv`s files or a bundled `h5` file. Until now the parser writes featuresets for *cells*, *perinuclei*, *nuclei*, *expandednuclei*,  *bacteria* and *invasomes*.\n* Query the meta DB using ``rnai-query`` and create and combine datasets. For that first meta files generated from the step above are written into a database. Then the DB can be queried against to subset single *genes*, *sirnas*, *pathogens*, etc. and write the *normalized* results.\n\n## Installation\n\nMake sure to have `python3` installed. `rnaiutilities` does not support\nprevious versions. The best way to do that is to download [anaconda](https://www.continuum.io/downloads) and create a\nvirtual [environment](https://conda.io/docs/using/envs.html).\n\nDownload the latest [release](https://github.com/dirmeier/rnaiutilities/releases) first and install it using:\n\n```bash\n  pip install .\n```\n\nIf you get errors, I probably forgot some dependency.\n\n## Documentation\n\nCheck out the documentation [here](https://rnaiutilities.readthedocs.io/en/latest/).\n\n## Author\n\nSimon Dirmeier \u003csimon.dirmeier@web.de\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdirmeier%2Frnaiutilities","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdirmeier%2Frnaiutilities","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdirmeier%2Frnaiutilities/lists"}