{"id":27335284,"url":"https://github.com/dcdanko/gimmebio","last_synced_at":"2026-02-27T15:39:32.090Z","repository":{"id":73643057,"uuid":"100515662","full_name":"dcdanko/gimmebio","owner":"dcdanko","description":null,"archived":false,"fork":false,"pushed_at":"2022-12-26T20:44:28.000Z","size":46829,"stargazers_count":2,"open_issues_count":2,"forks_count":3,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-12T14:51:56.062Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/dcdanko.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2017-08-16T17:34:00.000Z","updated_at":"2021-11-26T07:38:11.000Z","dependencies_parsed_at":null,"dependency_job_id":"590a8aea-c867-4d36-906f-a21c4f543be8","html_url":"https://github.com/dcdanko/gimmebio","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dcdanko/gimmebio","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcdanko%2Fgimmebio","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcdanko%2Fgimmebio/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcdanko%2Fgimmebio/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcdanko%2Fgimmebio/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dcdanko","download_url":"https://codeload.github.com/dcdanko/gimmebio/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcdanko%2Fgimmebio/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29902043,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-27T14:46:13.553Z","status":"ssl_error","status_checked_at":"2026-02-27T14:46:10.522Z","response_time":57,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2025-04-12T14:47:40.428Z","updated_at":"2026-02-27T15:39:32.085Z","avatar_url":"https://github.com/dcdanko.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"gimmebio\n========\n\n.. image:: https://img.shields.io/pypi/v/gimmebio.svg\n        :target: https://pypi.python.org/pypi/gimmebio\n\n.. image:: https://circleci.com/gh/dcdanko/gimmebio.svg?style=svg\n    :target: https://circleci.com/gh/dcdanko/gimmebio\n\n.. image:: https://www.codefactor.io/Content/badges/A.svg\n    :target: https://www.codefactor.io/repository/github/dcdanko/gimmebio\n\nUtilities and explorations in computational Biology. MIT License.\n\nPackages\n--------\n\n- Kmers, make kmers of many different styles.\n- Linked Reads, utilities for handling linked read data\n- Seqs, general utilites for handling sequence data. Some IO which should be deprecated\n- Bayesian First Aid, incomplete python implementation of bfa_\n- Hiveplots, python implemnetation of hiveplots with area hiveplots\n- operonator, experiment using linked reads to detect gene clusters\n- ponce_de_leon, experiment using Approx Bayesian Computation to bridge low complexity regiosn\n- ram_seq, use Ramanujan-Fourier transform to process sequence data\n- seqtalk, experiment with neural nets for sequence processing\n- taxa_ags_normalizer, estimate average genome size for taxa\n\nInstallation\n------------\n\n\nInstall from PyPi.\n\n.. code-block:: bash\n\n    pip install gimmebio\n\nInstall from source.\n\n.. code-block:: bash\n\n    git clone git@github.com:dcdanko/gimmebio.git\n    cd gimmebio\n    python setup.py install\n\n\nCredits\n-------\n\n\nThis package is structured as a set of microlibraries_\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n`gimmebio` was written by `David C. Danko \u003cdcdanko@gmail.com\u003e`_.\n\n.. _bfa: https://github.com/rasmusab/bayesian_first_aid\n.. _metadata: https://github.com/MetaSUB/MetaSUB-metadata\n.. _metagenscope: https://www.metagenscope.com/\n.. _microlibraries: https://blog.shazam.com/python-microlibs-5be9461ad979\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _AWS-CLI: https://docs.aws.amazon.com/cli/latest/userguide/installing.html\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdcdanko%2Fgimmebio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdcdanko%2Fgimmebio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdcdanko%2Fgimmebio/lists"}