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

Hello everyone,

As our projects diversify past the core majiq and voila components, we aim to provide a centralized support environment for all of the projects together. As such, when asking a question please remember to add a specific label to describe your question so it's easier to differentiate. Feel free to add new labels if one covering your topic exactly does not already exist.

Biociphers Team.

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We just released a new update for MAJIQ 2 branch. MAJIQ 2.2 has a number of improvements and fixes in many edge cases during the majiq build process, as well as incremental build mode. In addition, there are small performance improvements, in majiq and voila and other new minor features.

Please see the full patch nodes and download details at the pinned thread here.

Thanks for your help and we hope you enjoy the new majiq, great new features are coming soon.

Biociphers Team.

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Hello everyone,

MAJIQ 2.0 has been released. It represents a significant upgrade compared to previous MAJIQ 1.1. Main advantages and changes include:

A significant gain in speed. This is the result of algorithmic improvements and porting much of the core to C++.
New algorithm for intron retention. The new algorithm is both faster and more accurate.
New visualization engine: The release includes VOILA 2.0 which is now run as local service. This allows for smoother/faster interaction and enhanced features such as a built in search option.
Output a negative set: When comparing two conditions MAJIQ can give not only a high confidence set of changing events but also a high confidence set of events that are *not* changing.

As a consequence of these changes, MAJIQ 2.0 can easily handle hundreds and even thousands of samples. Most importantly, 2.0 serves as a base for many exciting new features and algorithms that support new use cases, so stay tuned!

Finally, while the academic license remains the same please note that commercial license has changed. Commercial users can keep using 1.1 as before, if they want to upgrade to MAJIQ 2.0 they should follow the instructions found on https://majiq.biociphers.org/commercial.php

MAJIQlopedia

Parham Habibzadeh