{"id":21287752,"url":"https://github.com/stjudecloud/mtsg","last_synced_at":"2025-07-29T18:09:26.324Z","repository":{"id":72438840,"uuid":"143784062","full_name":"stjudecloud/mtsg","owner":"stjudecloud","description":"Find and quantify COSMIC mutational signatures across samples","archived":false,"fork":false,"pushed_at":"2023-07-06T20:15:47.000Z","size":489,"stargazers_count":2,"open_issues_count":1,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-22T05:28:48.953Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","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/stjudecloud.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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":"2018-08-06T21:15:03.000Z","updated_at":"2021-05-14T19:02:16.000Z","dependencies_parsed_at":null,"dependency_job_id":"1257b0f7-5675-42d1-92bc-19b492e0399b","html_url":"https://github.com/stjudecloud/mtsg","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fmtsg","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fmtsg/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fmtsg/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fmtsg/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stjudecloud","download_url":"https://codeload.github.com/stjudecloud/mtsg/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243748053,"owners_count":20341628,"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":[],"created_at":"2024-11-21T12:15:37.775Z","updated_at":"2025-03-15T15:25:38.066Z","avatar_url":"https://github.com/stjudecloud.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Mutational Signatures\n\n**Mutational Signatures** (abbreviated as **mtsg**) finds and quantifies [COSMIC\nmutational signatures] across samples.\n\nmtsg uses a base set of mutational signatures extracted by [SigProfiler] for\n[single-base substitutions] (SBS), i.e., single-nucleotide variants (SNV),\nusing 2780 whole-genome variant calls from the ICGC/TCGA [Pan-Cancer Analysis\nof Whole Genomes] (PCAWG) project.\n\n[COSMIC mutational signatures]: https://cancer.sanger.ac.uk/cosmic/signatures\n[SigProfiler]: https://cancer.sanger.ac.uk/cosmic/signatures/sigprofiler.tt\n[single-base substitutions]: https://cancer.sanger.ac.uk/cosmic/signatures/SBS/index.tt\n[Pan-Cancer Analysis of Whole Genomes]: https://dcc.icgc.org/pcawg\n\n## Prerequisites\n\n  * [Python] ^3.8\n    * [sigproSS] ^0.0.0\n\n[Python]: https://www.python.org/\n[sigproSS]: https://github.com/AlexandrovLab/SigProfilerSingleSample\n\n## Install\n\nUse [Poetry] to install mtsg and its dependencies.\n\n```\n$ poetry install --no-dev\n```\n\n`mtsg init` can then be used to install base mutational matrices given a\nsupported genome build.\n\n```\n$ mtsg init --genome-build \u003cgenome-build\u003e\n```\n\nReplace `\u003cgenome-build\u003e` with one of `GRCh37`, `GRCh38` (Homo sapiens),\n`mm9`, `mm10` (Mus musculus), or `rn6` (Rattus norvegicus).\n\n[Poetry]: http://python-poetry.org/\n\n## Usage\n\nMutational Signatures is installed as the executable `mtsg`. It has three\ncommands: `init`, `run`, and `visualize`.\n\n### Run\n\n`run` is used to profile samples (as VCFs) using known mutational signatures.\nThe selected genome build must match the input VCFs and previously installed\nduring the installation.\n\n```\nusage: mtsg run [-h] [--dst-prefix DST_PREFIX] [--genome-build {GRCh37,GRCh38,mm9,mm10,rn6}] src-prefix\n\npositional arguments:\n  src-prefix\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --dst-prefix DST_PREFIX\n  --genome-build {GRCh37,GRCh38,mm9,mm10,rn6}\n```\n\n### Visualize\n\n`visualize` uses signature activities (generated by `run` and typically named\n`Sig_activities.txt`) to create an interactive plot.\n\n```\nusage: mtsg visualize [-h] --reference REFERENCE --output OUTPUT src\n\npositional arguments:\n  src\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --reference REFERENCE\n  --output OUTPUT\n```\n\n## Docker\n\nMutational Signatures has a `Dockerfile` to create a container image, which\nsets up and installs the required runtime and dependencies. It installs\nreference files for only GRCh38 and uses COMSIC mutational signatures 3.1. To\nbuild and use this image, [install Docker](https://docs.docker.com/install)\nfor your platform.\n\n### Build\n\nIn the Mutational Signatures project directory, build the container image.\n\n```\n$ docker image build --tag mtsg .\n```\n\n### Run\n\nThe image uses `mtsg` as its entrypoint, giving access to all commands.\n\n```\n$ docker container run mtsg \u003cargs...\u003e\n```\n\nFor example, a typical workflow is to run the `run` command followed by `visualize`.\n\n```\n$ docker container run \\\n  --rm \\\n  --mount type=bind,source=$PWD/data,target=/data \\\n  --mount type=bind,source=$PWD/results,target=/results \\\n  mtsg \\\n  run \\\n  --dst-prefix /results \\\n  /data\n\n$ docker container run \\\n  --rm \\\n  --mount type=bind,source=$PWD/references,target=/references,readonly \\\n  --mount type=bind,source=$PWD/results,target=/results \\\n  mtsg \\\n  visualize \\\n  --reference /references/reference.tsv \\\n  --output /results/signatures.html \\\n  /results/Sig_activities.txt\n```\n\n## References\n\n  * Alexandrov, L.B., Kim, J., Haradhvala, N.J. _et al_. The repertoire of\n    mutational signatures in human cancer. _Nature_ **578**, 94–101 (2020).\n    https://doi.org/10.1038/s41586-020-1943-3\n\n  * Bergstrom, E.N., Huang, M.N., Mahto, U. _et al_.\n    SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns\n    of small mutational events. _BMC Genomics_ **20**, 685 (2019).\n    https://doi.org/10.1186/s12864-019-6041-2\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Fmtsg","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstjudecloud%2Fmtsg","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Fmtsg/lists"}