{"id":19434754,"url":"https://github.com/edawson/assisi","last_synced_at":"2026-06-17T11:31:29.717Z","repository":{"id":150735577,"uuid":"105075534","full_name":"edawson/assisi","owner":"edawson","description":"A somatic mutation signature simulator","archived":false,"fork":false,"pushed_at":"2020-02-13T18:12:36.000Z","size":89,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-11-19T11:03:18.250Z","etag":null,"topics":["autoencoders","mutational-signatures","simulation","snvs"],"latest_commit_sha":null,"homepage":null,"language":"Python","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/edawson.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":"2017-09-27T22:24:28.000Z","updated_at":"2020-02-13T18:12:38.000Z","dependencies_parsed_at":"2023-04-13T12:33:08.810Z","dependency_job_id":null,"html_url":"https://github.com/edawson/assisi","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/edawson/assisi","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fassisi","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fassisi/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fassisi/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fassisi/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/edawson","download_url":"https://codeload.github.com/edawson/assisi/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/edawson%2Fassisi/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34447264,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-17T02:00:05.408Z","response_time":127,"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":["autoencoders","mutational-signatures","simulation","snvs"],"created_at":"2024-11-10T14:47:22.667Z","updated_at":"2026-06-17T11:31:29.700Z","avatar_url":"https://github.com/edawson.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"assisi: another somatic signature simulator\n-------------------------------------------\nEric T. Dawson  \nSeptember 27 2017\n\n\n## What is it?\n`assisi` is a python package that simulates mutational signature profiles (i.e. counts / proportions of trinucleotide context mutations) using Monte Carlo simulation.\n\n## Required / useful files\nWe've included the cosmic mutational signatures probabilities from deconstructSigs (https://github.com/raerose01/deconstructSigs).\n\n## Running assisi\n`python assisi.py -h` for help.  \n\n## Typical usage: \nThe following command will generate a single mutational catalog with 1000 total mutations.\n`-r` specifies that assisi should generate a random number of signatures (1-10) and assign\nrandom proportions to each of those ten signatures. The sum of the proportions is 1.0,\nwith some error.  \n`-i` is the COSMIC SBS96 mutational context probabilities; each row is a signature, and each column\nis the proportion of that mutational context in the signature.\n\n```\npython assisi.py -i cosmic_file.tsv -n 1000 -r \u003e catalog.tsv\n```\n\nRules for COSMIC sig files:  \n    No headers  \n    Tab separated  \n    No restriction on number of rows  \n    There must be 96 columns (for now)  \n\n\nThe next version of assisi will use a tidy format for this data.\n\nThe output of assisi when run as above is a single line with the following columns:  \n```\n\u003cnumber of signatures\u003e \u003cPython dictionary of signature : proportion\u003e \u003cfirst context count\u003e ... \u003clast context count\u003e\n```\n\nMultiple catalogs can be generated by passing the `-m` flag and a desired number of catalogs:\n```\n## Simulate 1000 catalogs\npython assisi.py -i cosmic_file.tsv -n 1000 -r -m 1000 \u003e catalogs.tsv\n```\n\nAssisi uses the Python multiprocessing package to optionally generate catalogs in parallel.\nWe recommend using this feature when simulating more than one catalog, as it decreases runtime\nproportional to the number of available compute cores and does not affect results in any way.\n```\n## Simulate 1000 catalogs, with 4 threads\npython assisi.py -i cosmic_file.tsv -n 1000 -r -m 1000 -t 4 \u003e catalogs.tsv\n```\n\n\n## Installation\n`assisi` is written in barebones python3 and is backwards-compatible with python 2.7 - no installation necessary.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedawson%2Fassisi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fedawson%2Fassisi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedawson%2Fassisi/lists"}