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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
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and
Twitter
.
Happy posting!
-The GenePattern team
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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
unread,
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
unread,
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
Joseph
,
Ted Liefeld
5
9/20/24
Browser Accessibility
Joseph, what server are you logging in to? They are still on cloud.genepattern.org. They are not and
unread,
Browser Accessibility
Joseph, what server are you logging in to? They are still on cloud.genepattern.org. They are not and
9/20/24
Xayah
,
Ted (aka John) Liefeld
2
9/18/24
ssGSEA download function
Clicking "Save file" will "save a copy of the file to your local computer". It
unread,
ssGSEA download function
Clicking "Save file" will "save a copy of the file to your local computer". It
9/18/24
ravi
, …
John Liefeld
5
9/17/24
STAR.aligner - Sample input
Hi Ted, Thank you for the information. It helps to plan the analysis timeline. Best regards, Ravi. On
unread,
STAR.aligner - Sample input
Hi Ted, Thank you for the information. It helps to plan the analysis timeline. Best regards, Ravi. On
9/17/24
ece janet dinc
, …
John Liefeld
10
9/17/24
DESq2 analysis error from GEOdataset
Got it! I will try and if I need to, I will start a new thread! Thanks a lot again for your help,
unread,
DESq2 analysis error from GEOdataset
Got it! I will try and if I need to, I will start a new thread! Thanks a lot again for your help,
9/17/24
ravi
,
John Liefeld
2
9/17/24
Seurat modules use - info request - Screenshot attached
Hi, I am not an expert in Seurat, but there is a GenePattern notebook that goes over the use of the
unread,
Seurat modules use - info request - Screenshot attached
Hi, I am not an expert in Seurat, but there is a GenePattern notebook that goes over the use of the
9/17/24
Lauren Dalvin
, …
Anthony Castanza
12
9/16/24
Error on pathway analysis
I think I got it!! Just had to remove spaces from the file name itself. Thank you so much for your
unread,
Error on pathway analysis
I think I got it!! Just had to remove spaces from the file name itself. Thank you so much for your
9/16/24
Ted (aka John) Liefeld
,
Ted Liefeld
2
9/16/24
Re: [gp-team] 502 bad gateway error
The server is available again now. PLease let us know if you have any further problems Ted
unread,
Re: [gp-team] 502 bad gateway error
The server is available again now. PLease let us know if you have any further problems Ted
9/16/24
Ted Liefeld
2
9/16/24
GenePattern server downtime 9/16/2024
Downtime is completed, the server is available again. On Monday, September 16, 2024 at 6:14:23 AM UTC
unread,
GenePattern server downtime 9/16/2024
Downtime is completed, the server is available again. On Monday, September 16, 2024 at 6:14:23 AM UTC
9/16/24
胡金桐
, …
Andrew Cherniack
8
9/14/24
Help letter,
Also, I don't know where you got your marker file from, but there needs to be an SNP at the end
unread,
Help letter,
Also, I don't know where you got your marker file from, but there needs to be an SNP at the end
9/14/24
Patricia Muskus
,
Anthony Castanza
5
9/10/24
Help with ssGSEA
Thanks Anthony, I went ahead and narrowed it down to two groups. I'm sorry for all the questions,
unread,
Help with ssGSEA
Thanks Anthony, I went ahead and narrowed it down to two groups. I'm sorry for all the questions,
9/10/24
Jennifer Diaz
,
Michael Reich
3
9/9/24
MAF requirements for MutSigCV
Hi Jennifer - you should submit the entire MAF file. Best, Michael On Fri, Sep 6, 2024 at 12:45 PM
unread,
MAF requirements for MutSigCV
Hi Jennifer - you should submit the entire MAF file. Best, Michael On Fri, Sep 6, 2024 at 12:45 PM
9/9/24
ravi
,
Michael Reich
3
9/6/24
Neoantigen detection
Hi Michael, Thank you for your reply and information. Best regards, Ravi. On Sat, 7 Sept 2024 at 03:
unread,
Neoantigen detection
Hi Michael, Thank you for your reply and information. Best regards, Ravi. On Sat, 7 Sept 2024 at 03:
9/6/24