majiq_voila

1–30 of 346

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

Harvey Che, Elsa Claude2

8:36 AM

LSV found in voila tsv but not in voila view

Hi, I have the same issue here. I'd also like to know the reason of such a difference. Thanks,

unread,

LSV found in voila tsv but not in voila view

Hi, I have the same issue here. I'd also like to know the reason of such a difference. Thanks,

8:36 AM

Esther Kockelmans, Paul Jewell25

7:09 AM

MAJIQ voila error

Hi Paul, I read the previous messages and saw the following steps! Thank you so much, it works and I

unread,

MAJIQ voila error

Hi Paul, I read the previous messages and saw the following steps! Thank you so much, it works and I

7:09 AM

Rupert Hugh-white, … Elsa Claude7

5:41 AM

LSV stringency parameters (min-experiments etc.)

Hi Matthew, Thanks a lot for the answer ! That is much more clear now. I'll find a way to

unread,

LSV stringency parameters (min-experiments etc.)

Hi Matthew, Thanks a lot for the answer ! That is much more clear now. I'll find a way to

5:41 AM

Sarah Djeddi, Matthew Gazzara2

Feb 24

voila tsv output error

Hi Sarah, Thank you for your interest. To get a bit more information in order to help you out, can

unread,

voila tsv output error

Hi Sarah, Thank you for your interest. To get a bit more information in order to help you out, can

Feb 24

Alexis W, Matthew Gazzara6

Feb 24

Running MAJIQ PSI on replicates

Hi Alexis, Glad to have helped and thank you for using / improving the tool with your questions!

unread,

Running MAJIQ PSI on replicates

Hi Alexis, Glad to have helped and thank you for using / improving the tool with your questions!

Feb 24

Alexander Dietrich, Paul Jewell13

Feb 19

voila tsv error

Hello Alex, These column definitions were removed in general, we we ended up not fully trusting them,

unread,

voila tsv error

Hello Alex, These column definitions were removed in general, we we ended up not fully trusting them,

Feb 19

Huck Thornton, Paul Jewell2

Feb 17

Error in labeling samples in config file

Hi Huck, It's not just about the naming. You can specify names with the dpsi call, which will

unread,

Error in labeling samples in config file

Hi Huck, It's not just about the naming. You can specify names with the dpsi call, which will

Feb 17

tya...@gmail.com, Paul Jewell2

Feb 17

How to get gene name list sorted by the column "dpsi per junction" in interacting voila ?

Hello, I'm still a little unsure your desired use case / function. You would like voila TSV

unread,

How to get gene name list sorted by the column "dpsi per junction" in interacting voila ?

Hello, I'm still a little unsure your desired use case / function. You would like voila TSV

Feb 17

aykut sen, Paul Jewell3

Feb 15

Majiq psi - AttributeError: 'str' object has no attribute 'dtype'

Hi Paul, Thank you for your response and recommendations. The build command took about 4-5 minutes to

unread,

Majiq psi - AttributeError: 'str' object has no attribute 'dtype'

Hi Paul, Thank you for your response and recommendations. The build command took about 4-5 minutes to

Feb 15

Huck Thornton, … mgaz...@biociphers.org4

Feb 11

How to interpret MAJIQ analysis figure??

Hi Huck, Sorry but the MAJIQ documentation you are referencing does seem to be incorrect. The text is

unread,

How to interpret MAJIQ analysis figure??

Hi Huck, Sorry but the MAJIQ documentation you are referencing does seem to be incorrect. The text is

Feb 11

Juliana Chu, … Paul Jewell9

Feb 11

Hi Juliana, I've ran these exact commands in a new, blank directory: $ git clone https://

unread,

Hi Juliana, I've ran these exact commands in a new, blank directory: $ git clone https://

Feb 11

Juliana Chu, Paul Jewell2

Feb 10

GFF3 error :incorrect gff

Hi Juliana, I'm thinking this is the same issue as the thread at https://groups.google.com/g/

unread,

GFF3 error :incorrect gff

Hi Juliana, I'm thinking this is the same issue as the thread at https://groups.google.com/g/

Feb 10

Álvaro Andrades, … Paul Jewell7

Feb 2

majiq installation successful, but executing majiq yields error

Hi, After days of trying to find out what was wrong in my system and Googling cryptic uninformative

unread,

majiq installation successful, but executing majiq yields error

Hi, After days of trying to find out what was wrong in my system and Googling cryptic uninformative

Feb 2

Huck Thornton, Paul Jewell4

Jan 29

Error with MAJIQ (possible failure to find BAM files?)

Hi Huck, It's not necessarily an error for a few genes, but if it's most of them, you may

unread,

Error with MAJIQ (possible failure to find BAM files?)

Hi Huck, It's not necessarily an error for a few genes, but if it's most of them, you may

Jan 29

myhoan...@gmail.com, Paul Jewell3

Jan 25

voila visualization, tsv content

Hi Paul, Thank you for your message! For 1) I think I'm looking at the one generated during majiq

unread,

voila visualization, tsv content

Hi Paul, Thank you for your message! For 1) I think I'm looking at the one generated during majiq

Jan 25

Elsa Claude, Paul Jewell6

Jan 22

Can't install majiq - error: invalid command 'bdist_wheel'

Awesome. I'm glad we were able to get this resolved! On Friday, January 22, 2021 at 4:24:17 AM

unread,

Can't install majiq - error: invalid command 'bdist_wheel'

Awesome. I'm glad we were able to get this resolved! On Friday, January 22, 2021 at 4:24:17 AM

Jan 22

salim megat, Paul Jewell2

Jan 20

majiq-spel issue

Hello Salim, Can you please include here the lsv-id / lsv link that you have generated _or_ the input

unread,

majiq-spel issue

Hello Salim, Can you please include here the lsv-id / lsv link that you have generated _or_ the input

Jan 20

Huck Thornton, Paul Jewell6

Jan 15

Error during MAJIQ/VOILA installation

Also, I should clarify that it looks like the MAJIQ installation "worked" (no error message

unread,

Error during MAJIQ/VOILA installation

Also, I should clarify that it looks like the MAJIQ installation "worked" (no error message

Jan 15

Huck Thornton, Paul Jewell2

Jan 8

Re: Error during MAJIQ installation

Hi Huck, Could you please add your reply to the original thread? Is is much easier to follow the flow

unread,locked,

Re: Error during MAJIQ installation

Hi Huck, Could you please add your reply to the original thread? Is is much easier to follow the flow

Jan 8

Angad Kumar, … Chen4

12/31/20

successfully installed majiq2.2 but not able to call majiq

Hi Melina, Thanks so much for your help and quick response! It seems to be working now. Chen On

unread,

successfully installed majiq2.2 but not able to call majiq

Hi Melina, Thanks so much for your help and quick response! It seems to be working now. Chen On

12/31/20

TM, … myhoan...@gmail.com9

12/27/20

Advice about a warning

Hello Caleb and Jordi. In order to get rid of the thousands of warnings I got while running majiq

unread,

Advice about a warning

Hello Caleb and Jordi. In order to get rid of the thousands of warnings I got while running majiq

12/27/20

12/8/20

huge spike in intron retention events between Majiq 1.1 and 2.0

Hi, Thank you so much for this great tool, its been a pleasure to explore all its features! I have

unread,

huge spike in intron retention events between Majiq 1.1 and 2.0

Hi, Thank you so much for this great tool, its been a pleasure to explore all its features! I have

12/8/20

Juliana Chu, Anna-Leigh Brown4

11/27/20

no matching bam/bai file found

At a guess, (sorry I'm not actually a majiq developer or anything) try bamdirs=/Users/ju.chu/

unread,

no matching bam/bai file found

At a guess, (sorry I'm not actually a majiq developer or anything) try bamdirs=/Users/ju.chu/

11/27/20

11/22/20

Hello! I am doing some research and would like to use majiq. Unfortunately, I only have a gtf version

unread,

Hello! I am doing some research and would like to use majiq. Unfortunately, I only have a gtf version

11/22/20

Zhaoliang Liu, Paul Jewell3

11/19/20

Segmentation fault: 11 on 2.2-e25c4ac

Hi Paul, Thank you very much! Unfortunately, I don't have access to *Nix HPC. Here is how I

unread,

Segmentation fault: 11 on 2.2-e25c4ac

Hi Paul, Thank you very much! Unfortunately, I don't have access to *Nix HPC. Here is how I

11/19/20

Denisa Bogdan, Paul Jewell6

11/12/20

MAJIQ build error: segmentation fault 11 when detecting LSVs

Hi Denisa, Thank you for checking on this. Unfortunately i'm not sure how to isolate this further

unread,

MAJIQ build error: segmentation fault 11 when detecting LSVs

Hi Denisa, Thank you for checking on this. Unfortunately i'm not sure how to isolate this further

11/12/20

11/9/20

Re: problems with installation

Hi, I have recently installed MAJIQ on my Mac (OSX Catalina). I was getting some different error

unread,

Re: problems with installation

Hi, I have recently installed MAJIQ on my Mac (OSX Catalina). I was getting some different error

11/9/20

Aoi W., Paul Jewell2

11/6/20

VOILA doesn't visualize certain LSVs

Hi Aoi, Thank you for the report. Remember that the filters in the voila summary table apply to ANY

unread,

VOILA doesn't visualize certain LSVs

Hi Aoi, Thank you for the report. Remember that the filters in the voila summary table apply to ANY

11/6/20

11/4/20

Problem with Voila

Hello, there! I run into errors with I try to use tsk and view command . For tsv: I ran: voila tsv /

unread,

Problem with Voila

Hello, there! I run into errors with I try to use tsk and view command . For tsv: I ran: voila tsv /

11/4/20

Juliana Chu, Paul Jewell5

11/4/20

KeyError: 'lsv_types is not a file in the archive'

Hello, Paul Yes! it did help! Thank you for your help! -Juliana On Wednesday, November 4, 2020 at 1:

unread,

KeyError: 'lsv_types is not a file in the archive'

Hello, Paul Yes! it did help! Thank you for your help! -Juliana On Wednesday, November 4, 2020 at 1:

11/4/20

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