WARNING: For some users, google groups seems to silently block/spam filter your message, even though it is legit. It will act like it sent but the message just vanishes. PLEASE SAVE/COPY your message locally, before sending it, just in case it gets destroyed. Then you can try to send again.

News 6-Jan-2026:

A recent update returns storage of data for annotated transcripts/TSS/TES back into the gff3 parsing step of v3's build, bring all functionality in line with historical releases. New versions should be able o read and process earlier v3 runs correctly but may produce a warning about missing annotated transcripts, which can be ignored.

News 20-June-2025:

V3 is out! It includes a complete change in the internals of the software. As with any complete rewrite, some slight bumps in the road are expected. I, and other members in the lab, will keep an eye on this board for any suggestions, questions, or bug reports. Please remember to check the bottom of installation instructions page for a method to install majiq v2 in the event you need to reproduce a prior analysis or use previously generated majiq / voila output files.

News 10-July-2024:

Patch, minor bugfixes, upgrades to many python libraries to more recent versions. The incompatibility with numpy 2.0.0 and the workarounds required below should now no longer be needed.

News 26-Jun-2024:

Numpy has released a change updating to version 2.0.0 recently which unfortunately seems to break some majiq dependencies. We will verify and resolve the new requirements soon, but as a quick fix in the meantime, simply run

$ pip install numpy==1.26.4

To revert the numpy version, which will requrn majiq to full functionality.

News 25-Jan-2024:

ATTENTION: a bug was discovered in version 2.5 of voila relating to the display of median read counts on the splicegraph in "voila view" interactive mode. The counts were incorrect for junctions with reads missing from some experiments. A hotfix has been released, please reinstall voila to update to the latest version.

News 20-Nov-2023:

Majiq 2.5 is out! Long reads + Short reads visualization mode, intergene junction detection, inline annotated transcripts, various visual + performance improvements and new features~!

News 27-Mar-2023:

Hi Everyone, today we distribute a new minor release version 2.41 which contains a few minor visual bug fixes and speedups, as well as a few new minor features such as new column outputs in voila tsv and modulize mode. Additionally, we now support python version 3.10 as an optional alternative to python version 3.8 which still remains the official tested version.

Thank you,

-San

Biociphers Team.

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Typo in majiq-v3 heterogen --help

Carolane Charest

San Jewell