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GenePattern Help Forum
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Welcome to the GenePattern help forum. This is a place to get help from GenePattern team members and fellow GenePattern users and also a place to post anything you've found useful in using GenePattern.
More information about GenePattern can be found at
https://genepattern.org
, where you can also sign up to follow us on
Facebook
and
Twitter
.
Happy posting!
-The GenePattern team
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soumithwork p
,
John Liefeld
2
Jun 16
error after installing module
Hi that looks like an error at run time not an error at the time of module installation. To debug
unread,
error after installing module
Hi that looks like an error at run time not an error at the time of module installation. To debug
Jun 16
Ted (aka John) Liefeld
May 8
Re: [gp-team] Log-in error
Courtney, Can you try again and confirm that this is happening repeatedly for you? I have just done a
unread,
Re: [gp-team] Log-in error
Courtney, Can you try again and confirm that this is happening repeatedly for you? I have just done a
May 8
Vered Bar
,
John Liefeld
3
Apr 29
Image view
Thanks!! Sent from my iPhone On 29 Apr 2025, at 17:48, John Liefeld <jlie...@cloud.ucsd.edu>
unread,
Image view
Thanks!! Sent from my iPhone On 29 Apr 2025, at 17:48, John Liefeld <jlie...@cloud.ucsd.edu>
Apr 29
Regan Odongo
, …
Kyle Starost
13
Apr 28
Q&A
Using GenePattern
Hi Ted, Thank you so much for the help! I changed it to a higher memory (12GB) and it worked. Much
unread,
Q&A
Using GenePattern
Hi Ted, Thank you so much for the help! I changed it to a higher memory (12GB) and it worked. Much
Apr 28
Subhojit paul
,
Ted Liefeld
2
Apr 2
DESeq2 ver 3 issues
Hi Sorry that this was missed when you sent this to gp-help originally. Unfortunately the job has
unread,
DESeq2 ver 3 issues
Hi Sorry that this was missed when you sent this to gp-help originally. Unfortunately the job has
Apr 2
Alexandra Glathar
,
Ted Liefeld
3
Mar 25
Error running SurvivalDifference and CoxRegression
Hi, SurvivalDifference is running again using the test data from the documentation (https://datasets.
unread,
Error running SurvivalDifference and CoxRegression
Hi, SurvivalDifference is running again using the test data from the documentation (https://datasets.
Mar 25
JESSIE HOLLINGSWORTH
,
Ted Liefeld
2
Mar 13
Increased storage
Hi, I have increased it back, sorry for the inconvenience. We upgraded the server last week, and
unread,
Increased storage
Hi, I have increased it back, sorry for the inconvenience. We upgraded the server last week, and
Mar 13
Jessie Hollingsworth
,
Ted Liefeld
4
Mar 5
Increased storage
Please refresh the page, you should see the update now. I assumed you were on cloud.genepattern.org
unread,
Increased storage
Please refresh the page, you should see the update now. I assumed you were on cloud.genepattern.org
Mar 5
Ted (aka John) Liefeld
Feb 26
Re: [gp-team] Log in error
Courtney, Sorry this is happening to you. Starting with the second error, the emails are case
unread,
Re: [gp-team] Log in error
Courtney, Sorry this is happening to you. Starting with the second error, the emails are case
Feb 26
Lilian Inoue
Feb 19
pmeTPM RNAseq data for running GSEA, ssGSEA and ssGSEA-ROC
Hi, My name is Lilian Inoue. I have a RNAseq dataset where the resulting reads were aligned to the
unread,
pmeTPM RNAseq data for running GSEA, ssGSEA and ssGSEA-ROC
Hi, My name is Lilian Inoue. I have a RNAseq dataset where the resulting reads were aligned to the
Feb 19
Pierre Laplante
,
Ted Liefeld
3
Feb 17
delivery error
Hi again, I don't yet have a fix but the problem seems to be that one or more of the files
unread,
delivery error
Hi again, I don't yet have a fix but the problem seems to be that one or more of the files
Feb 17
Andy Jia
Feb 13
Help with ssGSEA errors with input .gct files
Hello, my input .gct gene expression files produce constant error files and process terminations on
unread,
Help with ssGSEA errors with input .gct files
Hello, my input .gct gene expression files produce constant error files and process terminations on
Feb 13
liat anabel
,
Andrew Cherniack
9
Jan 31
Cross chromosomes error in GISTIC2.0 v. 6.15.30 unsing GenePattern public server
Thank you I will check this. Best regards, Liat בתאריך יום ו׳, 31 בינו׳ 2025, 23:39, מאת 'Andrew
unread,
Cross chromosomes error in GISTIC2.0 v. 6.15.30 unsing GenePattern public server
Thank you I will check this. Best regards, Liat בתאריך יום ו׳, 31 בינו׳ 2025, 23:39, מאת 'Andrew
Jan 31
Shota Kato
,
Andrew Cherniack
3
Jan 28
GISTIC2 with public server
Hello Andy, I used the default parameters with the broad analysis option. I attached the input seg
unread,
GISTIC2 with public server
Hello Andy, I used the default parameters with the broad analysis option. I attached the input seg
Jan 28
Anne Van Arsdale
,
Jens Luebeck
2
Jan 21
Amplicon Architect
Hi Anne, Thanks for reaching out with this bug report. The issue is related to the use of the
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Amplicon Architect
Hi Anne, Thanks for reaching out with this bug report. The issue is related to the use of the
Jan 21
ravi
,
Michael Reich
5
Jan 14
AmpliconSeq - FASTQ files - Analysis Tools
Thank you, Michael. Looks like the input MAFs are only from WGS or WES but not from Targeted Amplicon
unread,
AmpliconSeq - FASTQ files - Analysis Tools
Thank you, Michael. Looks like the input MAFs are only from WGS or WES but not from Targeted Amplicon
Jan 14
Xiao LIANG
, …
John Liefeld
7
12/10/24
AuDIT is not in the module list
Hi John and Ted, Thanks for the kind help! Best Regards, Xiao On Wed, Dec 11, 2024 at 6:02 AM John
unread,
AuDIT is not in the module list
Hi John and Ted, Thanks for the kind help! Best Regards, Xiao On Wed, Dec 11, 2024 at 6:02 AM John
12/10/24
Sumithra Sankararaman
,
Ted Liefeld
2
12/2/24
error running mutsigcv
I suggest you contact the authors of the method at mutsi...@broadinstitute.org and ask them. Hope
unread,
error running mutsigcv
I suggest you contact the authors of the method at mutsi...@broadinstitute.org and ask them. Hope
12/2/24
Mohammad Shboul
,
Ted Liefeld
2
11/20/24
BAM file around 40 GB
Hi, I can expand your quota, but I will need your username to do so. I did not find an account on
unread,
BAM file around 40 GB
Hi, I can expand your quota, but I will need your username to do so. I did not find an account on
11/20/24
lucy stead
11/15/24
Is it still possible to run ABSOLUTE?
Hi, we'd like to run ABSOLUTE for tumour purity estimation but I can't seem to find/access
unread,
Is it still possible to run ABSOLUTE?
Hi, we'd like to run ABSOLUTE for tumour purity estimation but I can't seem to find/access
11/15/24
Imran Noorani
,
Michael Reich
3
10/23/24
Mutect2
Hi Michael This is very helpful thank you Best wishes Imran Sent from my iPhone On 22 Oct 2024, at 22
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Mutect2
Hi Michael This is very helpful thank you Best wishes Imran Sent from my iPhone On 22 Oct 2024, at 22
10/23/24
Bob Zimmermann
,
Anthony Castanza
3
10/14/24
Normalization Strategies for ssGSEA
Thanks Anthony. This is helpful! Let me know if you hear anything further. On Friday, October 11,
unread,
Normalization Strategies for ssGSEA
Thanks Anthony. This is helpful! Let me know if you hear anything further. On Friday, October 11,
10/14/24
Alex Waldman
,
Anthony Castanza
2
10/11/24
Gene Priorization
Hi Alex, I'm not entirely sure what you're referring to here. We don't, to my knowledge,
unread,
Gene Priorization
Hi Alex, I'm not entirely sure what you're referring to here. We don't, to my knowledge,
10/11/24
Ariyan
,
Anthony Castanza
4
10/9/24
Missing genesets in ssGSEA Output Despite Being Present in Input Files
Hi Airyan, That's my bad, ssGSEA is actually located in the GSEA org repository not the
unread,
Missing genesets in ssGSEA Output Despite Being Present in Input Files
Hi Airyan, That's my bad, ssGSEA is actually located in the GSEA org repository not the
10/9/24
ali pirani
,
John Liefeld
2
10/8/24
Subscripted assignment dimension mismatch.
Hi, I took a quick look but am not familiar enough with MutSigCV to be able to help with this. I
unread,
Subscripted assignment dimension mismatch.
Hi, I took a quick look but am not familiar enough with MutSigCV to be able to help with this. I
10/8/24
Jennifer Diaz
,
Ted Liefeld
10
10/4/24
MutSigCV error
Jennifer, We don't have any prepared instructions but it should be possible to do assuming you
unread,
MutSigCV error
Jennifer, We don't have any prepared instructions but it should be possible to do assuming you
10/4/24
ravi
,
Michael Reich
5
9/24/24
Regd DiSCoVER
Thank you, Michael. Best regards, Ravi. On Wed, 25 Sept 2024 at 06:31, Michael Reich <mmreich@
unread,
Regd DiSCoVER
Thank you, Michael. Best regards, Ravi. On Wed, 25 Sept 2024 at 06:31, Michael Reich <mmreich@
9/24/24
ravi
,
Ted Liefeld
2
9/23/24
Job id: 604988 - Error
Ravi, based off the error it looks like the csv files are possibly corrupted or are somehow
unread,
Job id: 604988 - Error
Ravi, based off the error it looks like the csv files are possibly corrupted or are somehow
9/23/24
bri colletti
,
Michael Reich
2
9/23/24
ExpressionFileCreator Error
Hi Bri, Can you describe the problems you are having? Also, if you were using the public GenePattern
unread,
ExpressionFileCreator Error
Hi Bri, Can you describe the problems you are having? Also, if you were using the public GenePattern
9/23/24
Admita
,
edh...@cloud.ucsd.edu
2
9/20/24
NTP
Hi, What's the Job ID for this result? Edwin On Thursday, September 19, 2024 at 9:41:16 PM UTC-7
unread,
NTP
Hi, What's the Job ID for this result? Edwin On Thursday, September 19, 2024 at 9:41:16 PM UTC-7
9/20/24