{"id":23300767,"url":"https://github.com/andrewdavidsmith/transferase","last_synced_at":"2025-10-10T12:38:33.549Z","repository":{"id":263536813,"uuid":"868589174","full_name":"andrewdavidsmith/transferase","owner":"andrewdavidsmith","description":"The transferase system for retrieving methylome data from methbase","archived":false,"fork":false,"pushed_at":"2025-09-19T22:13:32.000Z","size":3946,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-29T09:03:03.852Z","etag":null,"topics":["bisulfite","bisulfite-sequencing","dna-methylation","epigenetics","epigenomics","methyl-seq","methylation","methylation-analysis","methylome","wgbs"],"latest_commit_sha":null,"homepage":"","language":"C++","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/andrewdavidsmith.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-10-06T19:01:30.000Z","updated_at":"2025-09-19T22:13:35.000Z","dependencies_parsed_at":"2024-12-31T05:19:39.721Z","dependency_job_id":"bd664325-b2d4-4edb-bcd1-273c78edf50c","html_url":"https://github.com/andrewdavidsmith/transferase","commit_stats":{"total_commits":910,"total_committers":1,"mean_commits":910.0,"dds":0.0,"last_synced_commit":"8c679f5ffc4fd7742a7ed2b3ebae7d49807f5916"},"previous_names":["andrewdavidsmith/mxe","andrewdavidsmith/transferase"],"tags_count":9,"template":false,"template_full_name":null,"purl":"pkg:github/andrewdavidsmith/transferase","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andrewdavidsmith%2Ftransferase","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andrewdavidsmith%2Ftransferase/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andrewdavidsmith%2Ftransferase/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andrewdavidsmith%2Ftransferase/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/andrewdavidsmith","download_url":"https://codeload.github.com/andrewdavidsmith/transferase/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andrewdavidsmith%2Ftransferase/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279003895,"owners_count":26083641,"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":"2025-10-10T02:00:06.843Z","response_time":62,"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":["bisulfite","bisulfite-sequencing","dna-methylation","epigenetics","epigenomics","methyl-seq","methylation","methylation-analysis","methylome","wgbs"],"created_at":"2024-12-20T09:19:19.079Z","updated_at":"2025-10-10T12:38:33.543Z","avatar_url":"https://github.com/andrewdavidsmith.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Transferase\n\n- [What is transferase](#what-is-transferase)\n- [What's new](#whats-new)\n- [Current status](#current-status)\n- [Installation](#installation)\n- [Command line app](docs/command_line.md)\n- [The Python package](docs/pyxfr.md)\n- [The R package](docs/Rxfr.md)\n- [All documentation](docs)\n\n## What is transferase?\n\nTransferase is a system for retrieving DNA methylation levels through\nuser-defined sets of genomic intervals. When analyzing whole-genome DNA\nmethylation profiles (\"methylomes\"), this form of summary statistic is central\nto both hypothesis testing and exploratory data analysis. In particular, it is\nthe basis of identifying differentially methylated regions, clustering\nmethylomes based on subsets of genes and other genomic features, and\nclustering genomic features according to their methylation dynamics.\n\nThe motivation behind transferase is simple. Methylomes derived from\nwhole-genome sequencing are huge. Even with access to high-performance\ncomputing, downloading, moving and processing a collection of methylomes takes\ntime. Any study leveraging this type of data will examine multiple different\nsets of genomic features and explore a variety of contrasts between\nmethylomes. This process can and should be faster and more convenient. But\nattaining these goals requires methods that synergize to exploit certain\nunique characteristics of sequencing-based whole-genome DNA methylation\nprofiles.\n\nTransferase is a complete system: it includes server software, a collection of\nfile formats and algorithms, client apps and APIs, all co-designed to maximize\nefficiency of data retrieval. Transferase can run on a local system for an\nindividual user, or remotely granting more users access to larger volumes of\ndata. With a good network connection, queries to a remote transferase server\ncan be faster than similar analysis of locally stored files.\n\nA public transferase server currently provides access to MethBase2, a\nmethylome database with roughly 14,000 vertebrate methylomes (as of\n2025-06-25) that are whole-genome, sequencing-based and *high-quality*. Most\nof these are split between human and mouse. The transferase clients include\ntools to help identify which among those methylomes might be useful to inform\nspecific biological questions.\n\n- If you work on Mac or Linux, there are lots of ways to get and use\n  transferase.\n\n- Transferase is in early development and is improving quickly.\n\n- But this means frequent changes -- check back for updates, and star or watch\n  this repo.\n\n- I appreciate your feedback. You can open an issue on GitHub or contact me\n  (Andrew) directly via the email in my GitHub profile.\n\n## What's new\n\n* **Important:** As of the release of v0.6.4, the format of future metadata\n  will no longer work with previous versions of `xfr select`.\n\n* **Important:** As of the release of v0.6.3, the server will not communicate\n  with previous versions.\n\n* Sliding window queries have been introduced in v0.6.3.\n\n* Remote query speed has been improved, and for \"bins\" or \"windows\" queries\n  this is by more than 3x.\n\n* The transferase Python package, pyxfr, can now be installed using\n  [pip](https://pypi.org/project/pyxfr/0.6.4) with Python \u003e= 3.12 on Linux\n  and macOS:\n  ```console\n  pip install pyxfr\n  ```\n\n## Current status\n\n- Public server: It's open and currently serving over 14,300 high-quality\n  methylomes. Right now (2025-07-17) the only restriction on use is that\n  individual queries are limited to roughly 45 methylomes, and roughly 1M\n  query intervals or bin/window size of 200bp. If you need more, do multiple\n  queries.\n\n- Linux: The binary installation for Linux should work on any Linux machine.\n\n- macOS: The binary installation for macOS should work on any Mac running at\n  least Ventura (macos-13; October 2022).\n\n- Python: The python package, pyxfr, can be installed with `pip install pyxfr`\n  and requires Python \u003e= 3.12 but otherwise should work on any Linux and\n  macOS-13 or later.\n\n- R: Rxfr can be installed on Linux and macOS (R \u003e= 4.4). Paste exactly this\n  into your terminal:\n  ```console\n  (CXX23=$(R CMD config CXX23) \u0026\u0026 [ -n \"$CXX23\" ] \u0026\u0026 $CXX23 --version)\n  ```\n  If you get output and it says version 14.2 or greater, you can install Rxfr\n  with devtools within R:\n  ```console\n  devtools::install_url('https://github.com/andrewdavidsmith/transferase/releases/download/v0.6.4/Rxfr_0.6.4.tar.gz')\n  ```\n  Alternatives for both Linux and macOS are covered in\n  [docs/installing_Rxfr.md](docs/installing_Rxfr.md).\n\n## Installation\n\n- **Linux**\n  The Linux binary releases should work on any Linux system. You\n  can find installers\n  [here](https://github.com/andrewdavidsmith/transferase/releases/v0.6.4),\n  including packages deb and rpm-based systems. The easiest is the\n  [shell installer](https://github.com/andrewdavidsmith/transferase/releases/download/v0.6.4/transferase-0.6.4-Linux.sh):\n  ```console\n  sh transferase-0.6.4-Linux.sh --prefix=/desired/install/location\n  /desired/install/location/bin/xfr  # check that it worked\n  ```\n\n- **Mac**\n  The transferase binary for Mac is a \"universal binary\" and\n  should work on any Mac. It is built to work on Ventura or later, but it has\n  worked on a much older system. The easiest is the\n  [shell installer](https://github.com/andrewdavidsmith/transferase/releases/download/v0.6.4/transferase-0.6.4-macOS.sh):\n  ```console\n  sh transferase-0.6.4-macOS.sh --prefix=/desired/install/location\n  /desired/install/location/bin/xfr  # check that it worked\n  ```\n\n- **Python**\n  pyxfr can be installed using\n  [pip](https://pypi.org/project/pyxfr/0.6.4) with Python (\u003e= 3.12) on Linux\n  and macOS:\n  ```console\n  pip install pyxfr\n  python3 -c \"from pyxfr import pyxfr; help(pyxfr)\"  # check that it worked\n  ```\n\n- **R**\n  Detailed instructions to install Rxfr are in\n  [docs/installing_Rxfr.md](docs/installing_Rxfr.md).\n\n- **Source** Detailed instructions for building from source are in\n  [docs/building.md](docs/building.md).\n\n- **Linux packages**\n  ```console\n  # Red Hat or Fedora (not sure SUSE has dnf)\n  rpm -i transferase-0.6.4-Linux.rpm              # See what will be installed\n  sudo dnf install ./transferase-0.6.4-Linux.rpm  # Install (note the dot-slash)\n  dnf info transferase                            # See what was installed\n  sudo dnf remove transferase                     # Uninstall\n\n  # Ubuntu or Debian\n  dpkg --info transferase-0.6.4-Linux.deb         # See what will be installed\n  sudo apt install ./transferase-0.6.4-Linux.deb  # Install (note the dot-slash)\n  apt info transferase                            # See what was installed\n  sudo apt remove transferase                     # Uninstall\n  ```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandrewdavidsmith%2Ftransferase","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fandrewdavidsmith%2Ftransferase","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandrewdavidsmith%2Ftransferase/lists"}