majiq_voila

1–30 of 432

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

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

chris chris, … Joseph Aicher3

Jun 28

Few questions about majiq and voila

With respect to strandedness: It's not a big deal if you have stranded data but run it unstranded

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Few questions about majiq and voila

With respect to strandedness: It's not a big deal if you have stranded data but run it unstranded

Jun 28

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.

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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-

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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

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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 <pjewell@biociphers.org

unread,

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

May 6

Sasha G, Paul Jewell2

Apr 27

Hi Sasha, Some versions of Mac OSX have had some issue with python3.8's multiprocessing library.

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Hi Sasha, Some versions of Mac OSX have had some issue with python3.8's multiprocessing library.

Apr 27

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

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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!

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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

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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

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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:

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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

Onkar Mulay, Paul Jewell3

Apr 2

RUN MAJIQ for simulated/synthetic data

sorry for late reply, but I have dropped that plan because gff3 looks quite a lot different On

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RUN MAJIQ for simulated/synthetic data

sorry for late reply, but I have dropped that plan because gff3 looks quite a lot different On

Apr 2

Giulia Tyzack, Matthew Gazzara2

Mar 31

No primers in MAJIQ-SPEL

Hi Giulia, You're right that these results seem strange and this could be a bug. Could you share

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No primers in MAJIQ-SPEL

Hi Giulia, You're right that these results seem strange and this could be a bug. Could you share

Mar 31

Mar 28

Installation errors

Hello, I am trying to install the package, but I keep running into an error. It seems the wheels for

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Installation errors

Hello, I am trying to install the package, but I keep running into an error. It seems the wheels for

Mar 28

arashdeep singh Sran, Paul Jewell3

Mar 24

star 2 pass v. star single pass

I'll forward another update: Different members of our lab have different preferences, so I think

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star 2 pass v. star single pass

I'll forward another update: Different members of our lab have different preferences, so I think

Mar 24

YINI LI, Paul Jewell2

Mar 17

installment seems successful, but encounter errors running majiq

Hello Yini, Have you created a virtualenv or conda env before installation? Can you brew install gcc-

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installment seems successful, but encounter errors running majiq

Hello Yini, Have you created a virtualenv or conda env before installation? Can you brew install gcc-

Mar 17

Ruhi Naik, … Paul Jewell5

Mar 17

Trouble Running MAJIQ Build

Hi Yini, Have you tried installing gcc and using the command line envvars as above? On Tuesday, March

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Trouble Running MAJIQ Build

Hi Yini, Have you tried installing gcc and using the command line envvars as above? On Tuesday, March

Mar 17

Noa Novershtern, Paul Jewell2

Mar 9

voila exit with "max() arg is an empty sequence" error

Hello Noa, Internally, this means that the program looked for exons in the splicegraph which should

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voila exit with "max() arg is an empty sequence" error

Hello Noa, Internally, this means that the program looked for exons in the splicegraph which should

Mar 9

Oliver Ziff, Paul Jewell5

Mar 7

MOCCASIN issues

Hi Oliver. I believe you'll likely find the answer is very much yes and themsome. I'd

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MOCCASIN issues

Hi Oliver. I believe you'll likely find the answer is very much yes and themsome. I'd

Mar 7

Carolin Brand, Paul Jewell3

Feb 28

Voila App for Windows

Hi Paul, Thanks, I found it, and it seems to be working just fine. Although I get the following

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Voila App for Windows

Hi Paul, Thanks, I found it, and it seems to be working just fine. Although I get the following

Feb 28

Lahat A, Paul Jewell2

Feb 18

some issue with voila tsv

Hello, I am supposing this is a difference in how the configparser library handles overrides for non

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some issue with voila tsv

Hello, I am supposing this is a difference in how the configparser library handles overrides for non

Feb 18

Lahat A, … Joseph Aicher4

Feb 16

Too many significant results

I am using the tsv that comes out of delta psi. I will check the output of "voila tsv" next

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Too many significant results

I am using the tsv that comes out of delta psi. I will check the output of "voila tsv" next

Feb 16

tsviya olender, … Lahat A3

Feb 16

Installation of Majiq didn't work

try installing h5py manually (https://docs.h5py.org/en/stable/build.html). However majiq requires

unread,

Installation of Majiq didn't work

try installing h5py manually (https://docs.h5py.org/en/stable/build.html). However majiq requires

Feb 16

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