{"id":23757761,"url":"https://github.com/broadinstitute/ichorcna","last_synced_at":"2025-04-09T11:12:19.766Z","repository":{"id":37276385,"uuid":"78222228","full_name":"broadinstitute/ichorCNA","owner":"broadinstitute","description":"Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.","archived":false,"fork":false,"pushed_at":"2024-03-20T13:29:09.000Z","size":11270,"stargazers_count":180,"open_issues_count":96,"forks_count":87,"subscribers_count":20,"default_branch":"master","last_synced_at":"2025-04-02T09:10:26.025Z","etag":null,"topics":["cell-free-dna","copy-number","low-coverage-sequencing"],"latest_commit_sha":null,"homepage":"","language":"R","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/broadinstitute.png","metadata":{"files":{"readme":"README.md","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}},"created_at":"2017-01-06T16:47:46.000Z","updated_at":"2025-03-24T13:18:25.000Z","dependencies_parsed_at":"2025-01-15T21:14:27.025Z","dependency_job_id":"01a4a19e-ce06-44e1-a30e-805ce9497611","html_url":"https://github.com/broadinstitute/ichorCNA","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/broadinstitute%2FichorCNA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2FichorCNA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2FichorCNA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2FichorCNA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","download_url":"https://codeload.github.com/broadinstitute/ichorCNA/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248027411,"owners_count":21035594,"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":["cell-free-dna","copy-number","low-coverage-sequencing"],"created_at":"2024-12-31T19:50:51.341Z","updated_at":"2025-04-09T11:12:19.747Z","avatar_url":"https://github.com/broadinstitute.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.com/broadinstitute/ichorCNA.svg?branch=master)](https://travis-ci.com/broadinstitute/ichorCNA)\n\n# *ichorCNA*\nichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing (ULP-WGS, 0.1x coverage). \n\n## ichorCNA Wiki Page\n**For more details on usage/pipelines, outputs, and FAQs, please visit the [GitHub Wiki page for ichorCNA](https://github.com/broadinstitute/ichorCNA/wiki)**\n\n## Description\nichorCNA uses a probabilistic model, implemented as a hidden Markov model (HMM), to simultaneously segment the genome, predict large-scale copy number alterations, and estimate the tumor fraction of a ultra-low-pass whole genome sequencing sample (ULP-WGS). \n\nThe methodology and probabilistic model are described in:  \nAdalsteinsson, Ha, Freeman, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. (2017) Nature Communications Nov 6;8(1):1324. [doi: 10.1038/s41467-017-00965-y](https://doi.org/10.1038/s41467-017-00965-y)\n\nThe analysis workflow consists of 2 tasks:  \n1. GC-content bias correction (using HMMcopy)  \n  a. Computing read coverage from ULP-WGS  \n  b. Data correction and normalization  \n3. CNA prediction and estimation of tumor fraction of cfDNA\n\n## Contacts\nIf you have any questions or feedback, please contact us at:  \n**Email:** \u003cichorcna@broadinstitute.org\u003e  \n**Google Group:** \u003chttps://groups.google.com/a/broadinstitute.org/forum/?fromgroups\u0026hl=en#!forum/ichorcna\u003e\n\n## Acknowledgements\nichorCNA is developed and maintained by Gavin Ha, Justin Rhoades, and Sam Freeman.  \n\nThis work was done in collaboration with  \n- **Blood Biopsy Group**, Group Leader **Viktor Adalsteinsson**, Broad Institute of MIT and Harvard\n- Laboratory of **Matthew Meyerson**, Medical Oncology, Dana-Farber Cancer Institute\n- Laboratory of **J. Christopher Love**, Koch Institute for integrative cancer research at MIT\n- Laboratory of **Gad Getz**, Cancer Program, Broad Institute\n\n## Software License\nichorCNA\nCopyright (C) 2017  Broad Institute\n\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License\nalong with this program.  If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbroadinstitute%2Fichorcna","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbroadinstitute%2Fichorcna","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbroadinstitute%2Fichorcna/lists"}