{"id":34049353,"url":"https://github.com/arosenfeld/immunedb","last_synced_at":"2026-04-09T03:33:56.563Z","repository":{"id":21982133,"uuid":"25307040","full_name":"arosenfeld/immunedb","owner":"arosenfeld","description":"ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data","archived":false,"fork":false,"pushed_at":"2024-05-21T19:31:28.000Z","size":15732,"stargazers_count":22,"open_issues_count":14,"forks_count":12,"subscribers_count":7,"default_branch":"master","last_synced_at":"2026-04-03T19:54:31.343Z","etag":null,"topics":["bioinformatics","database","immunology","python"],"latest_commit_sha":null,"homepage":"http://immunedb.com","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"plumbok/plumbok","license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/arosenfeld.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.txt","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}},"created_at":"2014-10-16T14:50:43.000Z","updated_at":"2025-11-22T02:14:03.000Z","dependencies_parsed_at":"2024-04-17T03:35:41.998Z","dependency_job_id":"05fc8dba-1713-4087-a92e-e920a55b3907","html_url":"https://github.com/arosenfeld/immunedb","commit_stats":{"total_commits":1185,"total_committers":4,"mean_commits":296.25,"dds":"0.11898734177215187","last_synced_commit":"7d369a2173a5076b1b9d74ea1cfd4d11054b354d"},"previous_names":[],"tags_count":70,"template":false,"template_full_name":null,"purl":"pkg:github/arosenfeld/immunedb","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arosenfeld%2Fimmunedb","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arosenfeld%2Fimmunedb/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arosenfeld%2Fimmunedb/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arosenfeld%2Fimmunedb/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/arosenfeld","download_url":"https://codeload.github.com/arosenfeld/immunedb/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arosenfeld%2Fimmunedb/sbom","scorecard":{"id":208158,"data":{"date":"2025-08-11","repo":{"name":"github.com/arosenfeld/immunedb","commit":"d1c4719ea2e62a6d1577cbff91455d64fb4a6509"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":3,"checks":[{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Code-Review","score":0,"reason":"Found 0/27 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/container.yaml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"License","score":9,"reason":"license file detected","details":["Info: project has a license file: LICENSE.txt:0","Warn: project license file does not contain an FSF or OSI license."],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/container.yaml:15: update your workflow using https://app.stepsecurity.io/secureworkflow/arosenfeld/immunedb/container.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/container.yaml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/arosenfeld/immunedb/container.yaml/master?enable=pin","Warn: containerImage not pinned by hash: Dockerfile:1: pin your Docker image by updating ubuntu:20.04 to ubuntu:20.04@sha256:8feb4d8ca5354def3d8fce243717141ce31e2c428701f6682bd2fafe15388214","Warn: npmCommand not pinned by hash: Dockerfile:33","Warn: pipCommand not pinned by hash: Dockerfile:58","Info:   0 out of   1 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   1 third-party GitHubAction dependencies pinned","Info:   0 out of   1 containerImage dependencies pinned","Info:   0 out of   1 npmCommand dependencies pinned","Info:   0 out of   1 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Vulnerabilities","score":6,"reason":"4 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: GHSA-3rq5-2g8h-59hc","Warn: Project is vulnerable to: GHSA-hc5x-x2vx-497g","Warn: Project is vulnerable to: GHSA-w3h3-4rj7-4ph4","Warn: Project is vulnerable to: GHSA-v9hf-5j83-6xpp"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 3 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}}]},"last_synced_at":"2025-08-17T00:12:09.986Z","repository_id":21982133,"created_at":"2025-08-17T00:12:09.986Z","updated_at":"2025-08-17T00:12:09.986Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31584656,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-08T14:31:17.711Z","status":"online","status_checked_at":"2026-04-09T02:00:06.848Z","response_time":112,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["bioinformatics","database","immunology","python"],"created_at":"2025-12-14T00:34:14.315Z","updated_at":"2026-04-09T03:33:56.558Z","avatar_url":"https://github.com/arosenfeld.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"ImmuneDB\n========\n\n[![Build Status](https://app.travis-ci.com/arosenfeld/immunedb.svg?branch=master)](https://app.travis-ci.com/arosenfeld/immunedb)\n[![Documentation Status](https://readthedocs.org/projects/immunedb/badge/?version=latest)](https://immunedb.readthedocs.io/en/latest/?badge=latest)\n[![codecov](https://codecov.io/gh/arosenfeld/immunedb/branch/master/graph/badge.svg)](https://codecov.io/gh/arosenfeld/immunedb)\n[![PyPI](https://img.shields.io/pypi/v/immunedb.svg)](https://pypi.python.org/pypi/ImmuneDB)\n[![Docker Pulls](https://img.shields.io/docker/pulls/arosenfeld/immunedb.svg)](https://hub.docker.com/r/arosenfeld/immunedb)\n[![](https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1\u0026message=compliant\u0026color=008AFF\u0026labelColor=000000\u0026style=plastic)](https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html)\n\nImmuneDB is a Python module that facilitates efficient storage and analysis of\nhigh-throughput B- and T-cell sequence data.\n\n# Documentation\nInstallation and usage instructions can be found at [immunedb.com](http://immunedb.com)\n\n# Support\nBasic questions regarding installing and running ImmuneDB can be emailed to\naaron.rosenfeld@pennmedicine.upenn.edu.  Bugs and feature requests should be\nsubmitted as [Issues](https://github.com/arosenfeld/immunedb/issues).  I try to\nrespond to both within 2 business days if possible.\n\n# Citing\nIf you use ImmuneDB, please cite the tool as:\n\nRosenfeld, A. M., Meng, W., Luning Prak, E. T., Hershberg, U., **ImmuneDB, a\nNovel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire\nSequencing Data**. Frontiers in Immunology **9** (2018).\n\nImmuneDB was originally announced previously in:\n\nRosenfeld, A. M., Meng, W., Luning Prak, E. T., Hershberg, U.,\n**ImmuneDB: a system for the analysis and exploration of high-throughput\nadaptive immune receptor sequencing data**, Bioinformatics **33** (2016), no. 2,\n292–293.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Farosenfeld%2Fimmunedb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Farosenfeld%2Fimmunedb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Farosenfeld%2Fimmunedb/lists"}