{"id":26359491,"url":"https://github.com/karchinlab/tcrtoolkit-sc","last_synced_at":"2026-02-17T12:34:54.171Z","repository":{"id":240409901,"uuid":"802548493","full_name":"KarchinLab/TCRtoolkit-SC","owner":"KarchinLab","description":"A NextFlow pipeline to process, analyze, and visualize single cell TCRseq data","archived":false,"fork":false,"pushed_at":"2024-05-18T16:31:25.000Z","size":379,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-18T15:48:59.148Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KarchinLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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}},"created_at":"2024-05-18T15:54:16.000Z","updated_at":"2024-05-18T16:31:28.000Z","dependencies_parsed_at":"2024-05-18T17:43:41.974Z","dependency_job_id":null,"html_url":"https://github.com/KarchinLab/TCRtoolkit-SC","commit_stats":null,"previous_names":["karchinlab/tcrtoolkit-sc"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/KarchinLab/TCRtoolkit-SC","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-SC","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-SC/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-SC/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-SC/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KarchinLab","download_url":"https://codeload.github.com/KarchinLab/TCRtoolkit-SC/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-SC/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29543907,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-17T12:21:34.159Z","status":"ssl_error","status_checked_at":"2026-02-17T12:21:02.057Z","response_time":100,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":"2025-03-16T15:59:54.729Z","updated_at":"2026-02-17T12:34:49.161Z","avatar_url":"https://github.com/KarchinLab.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# TCRtoolkit-SC: scTCR repertoire analysis\n\n![TCRtoolkit-banner](./assets/images/TCRtoolkit-banner.png)\n\nThanks for checking out `TCRtoolkit-SC`, a platform for single cell T Cell Repertoire analysis! `TCRtoolkit-SC` is wrapped in NextFlow, written in python, and uses Docker to manage dependencies.\n\nWe are currently working on developing a pipeline to take single cell TCRseq data and perform pseudobulk analysis similar to that of `TCRtoolkit-Bulk`.\n\n##  Requirements\n\n1. Nextflow\n\nNextflow can be used on any POSIX-compatible system (Linux, OS X, WSL). It requires Bash 3.2 (or later) and Java 11 (or later, up to 18) to be installed.\n\n```{bash}\nwget -qO- https://get.nextflow.io | bash\nchmod +x nextflow\n```\n\nThe nextflow executable is now available to run on the command line. The executable can be moved to a directory in your $PATH variable so you can run it from any directory.\n\n2. Docker\n\n`TCRtoolkit-SC` runs in Docker containers available [here](https://hub.docker.com/repository/docker/domebraccia/bulktcr/general). Depending on what operating system you are running (Linux, MacOS, WSL), please refer to the [Docker documentation](https://docs.docker.com/engine/install/) for installation instructions.\n\n3. TCRtoolkit\n\n```{bash}\ngit clone https://github.com/KarchinLab/TCRtoolkit-SC.git\ncd TCRtoolkit-SC\n```\n\n\n## Quick Start\n\nTBD","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarchinlab%2Ftcrtoolkit-sc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkarchinlab%2Ftcrtoolkit-sc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarchinlab%2Ftcrtoolkit-sc/lists"}