v0.6.2

What's changed

• Queries can accept more options to customize output formats.
• Users can customize how methylome are named in query output, allowing for project-relevant naming.
• The select command now supports methylome groups defined by users.
• Improvements to server performance and stability.
• Bug fixes related to error codes shown to users on invalid or inconsistent queries.

How to get transferase

Command line app

Linux

• transferase-0.6.2-Linux.sh
• transferase-0.6.2-Linux.tar.gz

macOS

• transferase-0.6.2-macOS.sh
• transferase-0.6.2-macOS.tar.gz

Linux packages

• transferase-0.6.2-Linux.rpm
• transferase-0.6.2-Linux.deb

Python

pip install pyxfr

R

Download Rxfr_0.6.2.tar.gz. Follow these instructions, which cover:

• macOS: R installed through either Homebrew or Conda
• Linux: R installed through either APT or Conda

While only these scenarios are covered in the instructions, for R >= 4.4, Rxfr can be installed on almost any macOS or Linux system.

Full Changelog: v0.6.1...v0.6.2

v0.6.1

What's Changed

• The transferase Python package is now on pypi.
• More details about available methylomes are displayed by the select command.
• The Python and R packages now include data frames with metadata about available methylomes.
• On macOS, one binary distribution covers all hardware/OS combinations.
• Binaries are built using GitHub Actions and public docker images, so the process is fully transparent.

How to get transferase

Command line tools

Linux

• transferase-0.6.1-Linux.sh
• transferase-0.6.1-Linux.tar.gz

macOS

• transferase-0.6.1-macOS.sh
• transferase-0.6.1-macOS.tar.gz

Linux packages

• transferase-0.6.1-Linux.rpm
• transferase-0.6.1-Linux.deb

Python

pip install pyxfr

R

Download Rxfr_0.6.1.tar.gz and follow these instructions. There are two options explained for Linux (Docker and Conda) and two options for macOS (Homebrew and Conda).

Full Changelog: v0.6.0...v0.6.1

v0.6.0

What's Changed

• Added the transferase R package (Rxfr)
• More output formats for command line queries
• More stable 'select' command for browsing methylomes

What file to download?

(Don't try to install from GitHub's auto-generated sources named "Source code".)

Get the command line tools

Linux:

• transferase-0.6.0-Linux.sh (easiest install)
• transferase-0.6.0-Linux.tar.gz

macOS:
(3 OS / hardware combinations, the first has worked for most users)

• transferase-0.6.0-macos-15-ARM64.sh
  transferase-0.6.0-macos-15-ARM64.tar.gz
• transferase-0.6.0-macos-14-ARM64.sh
  transferase-0.6.0-macos-14-ARM64.tar.gz
• transferase-0.6.0-macos-13-X64.sh
  transferase-0.6.0-macos-13-X64.tar.gz

Linux packages:

• transferase-0.6.0-Linux.rpm
• transferase-0.6.0-Linux.deb

Get the Python package

OS	Hardware	Python	Filename
Linux	x86_64	3.13	transferase-0.6.0-cp313-none-manylinux_2_17_x86_64.whl
		3.12	transferase-0.6.0-cp312-none-manylinux_2_17_x86_64.whl
macOS-15	M1/2/3	3.13	transferase-0.6.0-cp313-none-macosx_15_0_arm64.whl
		3.12	transferase-0.6.0-cp312-none-macosx_15_0_arm64.whl
macOS-14	M1/2/3	3.13	transferase-0.6.0-cp313-none-macosx_14_0_arm64.whl
		3.12	transferase-0.6.0-cp312-none-macosx_14_0_arm64.whl
macOS-13	x86_64	3.13	transferase-0.6.0-cp313-none-macosx_13_0_x86_64.whl
		3.12	transferase-0.6.0-cp312-none-macosx_13_0_x86_64.whl

Get the R package

One file: Rxfr_0.6.0.tar.gz

Full Changelog: v0.5.0...v0.6.0

v0.5.0

Overview

• The server is online so transferase can be used by anyone. Follow the instructions in docs/command_line.md
• Binaries are available for Linux (should work on any Linux) and for macOS, both x86 and ARM64.
• The Python API is available as a wheel for both Linux and macOS. It needs Python 3.12 or 3.13.
• Yes. The documentation is still terrible.

Full Changelog: v0.4.0...v0.5.0

v0.4.0

Overview

• This release is for testing purposes.
• The server is not public, so if you are testing this v0.4.0 you will have received information from me about it. The server is almost ready.
• The Linux binaries should work on almost any Linux. Unless you are doing a system-wide install, start by downloading the .sh and

sh transferase-0.4.0-Linux.sh

• The macOS binaries are only for x86 in this release.
• The Python API should work on any Linux, but probably only with Python 3.12. Install from the whl file in a venv with

pip install transferase-0.4.0-cp312-none-manylinux_2_17_x86_64.whl

• On macOS, the Python library is also restricted to x86 for now.
• Brief Python API examples can be found in the docs directory of the source repo.
• The sparse docs available are not yet packaged with the distributions. As they are written they will be added to the source repo.
• If you want to help, the biggest help you can give right now is just to attempt to run the binaries and just submit an issue when things break.

What's Changed

• Too many things...

Full Changelog: v0.3.0...v0.4.0

v0.3.0

What's Changed

• A lot has changed, but this release is still for debugging purposes.

Full Changelog: v0.2.0...v0.3.0

v0.2.0

First Release

I'm making this release for testing purposes. Check back -- more to come!