majiq_voila

1–30 of 444

Hello everyone,

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.

------

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

0 selected

Katie Saund, San Jewell2

Oct 20

Download all HTMLs for Voila View?

Hi Katie, As the browser rendering engine is required to display the gene pages as seen, there is not

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Download all HTMLs for Voila View?

Hi Katie, As the browser rendering engine is required to display the gene pages as seen, there is not

Oct 20

Hannah, San Jewell2

Sep 29

ERROR: Could not build wheels for rna-majiq

Hi Hannah, This is a problem with the OSX clang compiler. It does not support automatic

unread,

ERROR: Could not build wheels for rna-majiq

Hi Hannah, This is a problem with the OSX clang compiler. It does not support automatic

Sep 29

Yiying Hu, San Jewell3

Sep 7

Hi Yiying, Please also check the new solution I posted on https://groups.google.com/g/majiq_voila/c/

unread,

Hi Yiying, Please also check the new solution I posted on https://groups.google.com/g/majiq_voila/c/

Sep 7

Tim Benke, San Jewell2

Sep 7

similar issue to Yiying with install

Hi Tim, I am still fairly sure this specific error you have posted is a python3.10 issue, as it only

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similar issue to Yiying with install

Hi Tim, I am still fairly sure this specific error you have posted is a python3.10 issue, as it only

Sep 7

chris chris, San Jewell4

Aug 19

Question regarding voila modulize output

Hi San, This is from a dpsi analysis. I've attached the event where this happens (

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Question regarding voila modulize output

Hi San, This is from a dpsi analysis. I've attached the event where this happens (

Aug 19

Aug 17

latest version of majiq

Hi! I was just wondering what is the latest version of Majiq? I found a docker container with version

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latest version of majiq

Hi! I was just wondering what is the latest version of Majiq? I found a docker container with version

Aug 17

Yiying Hu, Paul Jewell3

Aug 2

clang: error: unsupported option '-fopenmp'

Hi Paul, Thank you so much for your reply. Unfortunately I met new problem. Preparing metadata (

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clang: error: unsupported option '-fopenmp'

Hi Paul, Thank you so much for your reply. Unfortunately I met new problem. Preparing metadata (

Aug 2

Maoting Chen, Paul Jewell7

Aug 1

Read count for junctions

Hi Paul, Thanks for your reply. I tried as you said and it did work. However, there is still

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Read count for junctions

Hi Paul, Thanks for your reply. I tried as you said and it did work. However, there is still

Aug 1

Sasha G, Paul Jewell4

Jul 29

unread,

Jul 29

Brian Joseph, Paul Jewell2

Jul 27

Intron offset error

Hello, To clarify is it the case that you believe the reads have actual errors which are being

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Intron offset error

Hello, To clarify is it the case that you believe the reads have actual errors which are being

Jul 27

Sasha G, … Paul Jewell4

Jul 27

Hi Hamrek, Can you please try one more switch? Instead of -j 1 can you try --debug? This should

unread,

Hi Hamrek, Can you please try one more switch? Instead of -j 1 can you try --debug? This should

Jul 27

Matthew Wright, Paul Jewell2

Jul 27

Question about dPSI threshold value

Hi Matt, Voila view provides both a raw dpsi value threshold and also statistical confidence

unread,

Question about dPSI threshold value

Hi Matt, Voila view provides both a raw dpsi value threshold and also statistical confidence

Jul 27

Ben J Draper, Paul Jewell2

Jul 27

Config file .ini file not being recognised using Singularity.

Hello Ben, Could you humor me and try first to put the absolute paths to settings.ini as well as DB.

unread,

Config file .ini file not being recognised using Singularity.

Hello Ben, Could you humor me and try first to put the absolute paths to settings.ini as well as DB.

Jul 27

chris chris, … Joseph Aicher5

Jul 15

Few questions about majiq and voila

Dear Chris, MAJIQ detects usage of different junctions/retained introns directly from split/unsplit

unread,

Few questions about majiq and voila

Dear Chris, MAJIQ detects usage of different junctions/retained introns directly from split/unsplit

Jul 15

Priyanka Mehta, Paul Jewell6

Jun 30

Trouble visualizing Majiq result in Viola.

Forgot to mention I am working on linux OS On Thu, Jun 30, 2022 at 9:48 AM Priyanka Mehta <

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Trouble visualizing Majiq result in Viola.

Forgot to mention I am working on linux OS On Thu, Jun 30, 2022 at 9:48 AM Priyanka Mehta <

Jun 30

Jun 18

MOCCASIN model matrix

Hi, I am working on differential splicing caused by 4 treatments, each with 6 replicates. From

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MOCCASIN model matrix

Hi, I am working on differential splicing caused by 4 treatments, each with 6 replicates. From

Jun 18

Kerr Welton, Paul Jewell2

Jun 10

voila tsv output description

Hello Kerr, I think you can find the description in general for these columns in the section here:

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voila tsv output description

Hello Kerr, I think you can find the description in general for these columns in the section here:

Jun 10

Maoting Chen, Paul Jewell5

Jun 6

gff3 file error in majiq build

Hi Paul, Thanks for your clarification. I think I can email the source to ask about the format.

unread,

gff3 file error in majiq build

Hi Paul, Thanks for your clarification. I think I can email the source to ask about the format.

Jun 6

Yong shan, Paul Jewell3

Jun 2

Discrepancy btwn voila view app and command line

Thank you for your quick reply! That explains it. I am using Windows 10 64-bit operating system, x64-

unread,

Discrepancy btwn voila view app and command line

Thank you for your quick reply! That explains it. I am using Windows 10 64-bit operating system, x64-

Jun 2

ЖИРАНДОЛЬ, Paul Jewell2

May 24

Voila modulize freezing in some cases

Hi Alex, This is very odd, and it a new issue, so you may need to help me with some debugging and

unread,

Voila modulize freezing in some cases

Hi Alex, This is very odd, and it a new issue, so you may need to help me with some debugging and

May 24

Yuxin Xu, Paul Jewell3

May 6

Hi Paul Thanks a lot, Best Yu-Xin On May 5, 2022, at 9:49 AM, Paul Jewell <pje...@biociphers.org

unread,

Hi Paul Thanks a lot, Best Yu-Xin On May 5, 2022, at 9:49 AM, Paul Jewell <pje...@biociphers.org

May 6

Onkar Mulay, Paul Jewell2

Apr 22

Multiple bam files of same patient

Hi Onkar, Can you describe your use case a bit more broadly? Which type of majiq quantifier did you

unread,

Multiple bam files of same patient

Hi Onkar, Can you describe your use case a bit more broadly? Which type of majiq quantifier did you

Apr 22

Sasha G, Paul Jewell10

Apr 20

error with BAM files

Ahh yes, for future readers I'm assuming the problem was the missing .bam.bai files used by

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error with BAM files

Ahh yes, for future readers I'm assuming the problem was the missing .bam.bai files used by

Apr 20

Apr 17

ERROR while installation : Failed building wheel for psutil/rna-majiq

I am having trouble installing majiq on Ubuntu 20.04. I am installing by downloading the repository

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ERROR while installation : Failed building wheel for psutil/rna-majiq

I am having trouble installing majiq on Ubuntu 20.04. I am installing by downloading the repository

Apr 17

Sasha G, Paul Jewell3

Apr 15

hg38 GFF3 format

Thank you, I did end up download from genecode. I downloaded the gff3 file for the chromosome. Now I

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hg38 GFF3 format

Thank you, I did end up download from genecode. I downloaded the gff3 file for the chromosome. Now I

Apr 15

Sasha G, Paul Jewell11

Apr 11

Please read this post, not the previous one (Installation errors)

Thank you, it worked!

unread,

Please read this post, not the previous one (Installation errors)

Thank you, it worked!

Apr 11

Apr 8

bug in config.py

Hi there, just to let you know the config optional section in the documentation does not work with

unread,

bug in config.py

Hi there, just to let you know the config optional section in the documentation does not work with

Apr 8

Onkar Mulay, Paul Jewell6

Apr 7

Combine multiple majiq outputs

Hi Onkar, I don't have a suggestion for that besides writing a custom script to transform the

unread,

Combine multiple majiq outputs

Hi Onkar, I don't have a suggestion for that besides writing a custom script to transform the

Apr 7

Kyle Drake, Paul Jewell3

Apr 7

Multiple sample comparison

Hi Paul, This is exactly what I was looking for, thank you very much! Best, Kyle On Thu, Apr 7, 2022

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Multiple sample comparison

Hi Paul, This is exactly what I was looking for, thank you very much! Best, Kyle On Thu, Apr 7, 2022

Apr 7

Oliver Ziff, … Paul Jewell7

Apr 7

majiq update queries | documentation | heterogen vs deltapsi | tsv output

Thanks Paul but no. I am plotting the output of heterogen as y-axis: -log10(tnom p-value) and x-axis:

unread,

majiq update queries | documentation | heterogen vs deltapsi | tsv output

Thanks Paul but no. I am plotting the output of heterogen as y-axis: -log10(tnom p-value) and x-axis:

Apr 7

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