{"id":32563026,"url":"https://github.com/smithlabcode/dnmtools","last_synced_at":"2025-10-29T02:56:23.700Z","repository":{"id":56711015,"uuid":"515744669","full_name":"smithlabcode/dnmtools","owner":"smithlabcode","description":"Tools for analyzing DNA methylation data","archived":false,"fork":false,"pushed_at":"2025-10-17T23:31:31.000Z","size":32124,"stargazers_count":43,"open_issues_count":31,"forks_count":10,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-10-18T03:45:57.752Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://dnmtools.readthedocs.io","language":"C++","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/smithlabcode.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"code_of_conduct.md","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,"zenodo":null,"notice":null,"maintainers":"MAINTAINERS.md","copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-07-19T21:20:36.000Z","updated_at":"2025-10-14T02:47:25.000Z","dependencies_parsed_at":"2023-12-15T02:30:45.441Z","dependency_job_id":"bd0d73f6-07e3-4dec-8fa2-d21a9876c1b0","html_url":"https://github.com/smithlabcode/dnmtools","commit_stats":null,"previous_names":[],"tags_count":16,"template":false,"template_full_name":null,"purl":"pkg:github/smithlabcode/dnmtools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fdnmtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fdnmtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fdnmtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fdnmtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/smithlabcode","download_url":"https://codeload.github.com/smithlabcode/dnmtools/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fdnmtools/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281549786,"owners_count":26520515,"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","status":"online","status_checked_at":"2025-10-29T02:00:06.901Z","response_time":59,"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":[],"created_at":"2025-10-29T02:56:08.545Z","updated_at":"2025-10-29T02:56:23.695Z","avatar_url":"https://github.com/smithlabcode.png","language":"C++","readme":"[![GitHub Downloads](https://img.shields.io/github/downloads/smithlabcode/dnmtools/total?style=social)](https://github.com/smithlabcode/dnmtools/releases)\n[![Install with Conda](https://anaconda.org/bioconda/dnmtools/badges/version.svg)](https://anaconda.org/bioconda/dnmtools)\n[![Install with Conda](https://anaconda.org/bioconda/dnmtools/badges/platforms.svg)](https://anaconda.org/bioconda/dnmtools)\n[![Install with Conda](https://anaconda.org/bioconda/dnmtools/badges/downloads.svg)](https://anaconda.org/bioconda/dnmtools)\n[![Documentation Status](https://readthedocs.org/projects/dnmtools/badge/?version=latest)](https://dnmtools.readthedocs.io/en/latest/?badge=latest)\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\nDNMTools is a set of tools for analyzing DNA methylation data from\nhigh-throughput sequencing experiments, especially whole genome bisulfite\nsequencing (WGBS), but also reduced representation bisulfite sequencing\n(RRBS). These tools focus on overcoming the computing challenges imposed by\nthe scale of genome-wide DNA methylation data, which is usually the early\nparts of data analysis.\n\n**Nanopore** As of v1.5.0, DNMTools has funcionality to start analysis with a\nBAM file from Nanopore sequencing with 5mC and 5hmC calls at CpG sites.\n\n## Usage\n\nThe documentation for DNMTools can be found\n[here](https://dnmtools.readthedocs.io).\n\n## Installation\n\n- **Linux**\n  [binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1-Linux.tar.gz).\n  Should work on any Linux distribution since roughly 2017.\n\n- **Mac**\n  [binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1-macOS.tar.gz).\n  Should work on any Mac hardware and macOS-13 (Ventura) or newer.\n\n- **Conda**\n  ```console\n  conda install -c bioconda dnmtools\n  ```\n\n- **Source**\n  [dnmtools-1.5.1.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1.tar.gz). Dependencies:\n  [GSL](http://www.gnu.org/software/gsl),\n  [HTSlib](https://github.com/samtools/htslib),\n  [libdeflate](https://github.com/ebiggers/libdeflate) and\n  [ZLib](https://github.com/madler/zlib). Installing HTSlib as a package\n  should also give you ZLib and libdeflate.  System-specific details below.\n\n  Build DNMTools like this:\n  ```console\n  tar -xf dnmtools-1.5.1.tar.gz\n  cd dnmtools-1.5.1\n  ./configure --prefix=$HOME\n  make\n  make install\n  ```\n\n  To get dependencies and a compiler on (these might with OS/package updates):\n\n  Ubuntu/Debian\n  ```console\n  apt-get install build-essential htslib-dev libgsl-dev\n  ```\n\n  RedHat/Fedora\n  ```console\n  dnf install @c-development @development-tools htslib-devel gsl-devel awk\n  ```\n\n  Homebrew (see notes below)\n  ```console\n  brew install gcc htslib gsl\n  ```\n\n  Conda (see notes below)\n  ```console\n  conda create -n build-env -c conda-forge -c bioconda \\\n      gcc gxx make autoconf automake htslib gsl zlib binutils \u0026\u0026 \\\n  conda activate build-env\n  ```\n\n  Notes: If you use only Homebrew or only Conda to setup your environment, you\n  could need additional dependencies, and some of what I listed you might\n  already have. You might need to set additional environment variables or run\n  configure differently. For example with Homebrew:\n  ```console\n  ./configure CPPFLAGS=\"-I$(brew --prefix)/include\" LDFLAGS=\"-L$(brew --prefix)/lib\"\n  ```\n\n## Contact\n\nAndrew D. Smith\nandrewds@usc.edu\n\n## Copyright and License Information\n\nCopyright (C) 2022-2025\n\nAndrew D. Smith and Guilherme de Sena Brandine\n\nAuthors of DNMTools: Andrew D. Smith and Guilherme de Sena Brandine\n\nEssential contributors: Ben Decato, Meng Zhou, Liz Ji, Terence Li, Jenny Qu,\nQiang Song, Fang Fang and Masaru Nakajima\n\nThis is free software: you can redistribute it and/or modify it under the\nterms of the GNU General Public License as published by the Free Software\nFoundation, either version 3 of the License, or (at your option) any later\nversion.\n\nThis software is distributed in the hope that it will be useful, but WITHOUT\nANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS\nFOR A PARTICULAR PURPOSE.  See the GNU General Public License for more\ndetails.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fdnmtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmithlabcode%2Fdnmtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fdnmtools/lists"}