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Mark
11/18/14
GLU help pages
Hi Just to let you know, the help documentation pages no longer link from the main glu page: https://
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GLU help pages
Hi Just to let you know, the help documentation pages no longer link from the main glu page: https://
11/18/14
Mark
,
Kevin Jacobs <jacobs@bioinformed.com>
3
4/24/14
dupcheck testpairs option
Hi I did some more tests, and it seems that to use the --testpairs option, the SNP data file must be
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dupcheck testpairs option
Hi I did some more tests, and it seems that to use the --testpairs option, the SNP data file must be
4/24/14
Mark
,
Kevin Jacobs <jacobs@bioinformed.com>
4
4/2/14
ibds vs dupcheck
Is there any way to do dupcheck without merging datasets? For example, I have dataset A which I know
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ibds vs dupcheck
Is there any way to do dupcheck without merging datasets? For example, I have dataset A which I know
4/2/14
Kevin Jacobs <jacobs@bioinformed.com>
12/20/12
Re: [glu-users] convert bed file to sdat file
Hi Jane, There is a bug in how monomorphic loci from PLINK are handled. I'll try to fix this in
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Re: [glu-users] convert bed file to sdat file
Hi Jane, There is a bug in how monomorphic loci from PLINK are handled. I'll try to fix this in
12/20/12
Mark
,
Kevin Jacobs <jacobs@bioinformed.com>
2
9/27/12
ld.surrogates
Hi Mark, You are correct -- the default minimum r2 is 0.15. I apologize that the version you have
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ld.surrogates
Hi Mark, You are correct -- the default minimum r2 is 0.15. I apologize that the version you have
9/27/12
Mark
8/16/12
genorepr
Hi I have a genotype file that is 'sort-of' in sdat format, but the SNPs are coded 0,1,2,
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genorepr
Hi I have a genotype file that is 'sort-of' in sdat format, but the SNPs are coded 0,1,2,
8/16/12
Mark
,
Jacobs, Kevin (NIH/NCI) [C]
2
8/13/12
forward stepwise regression
Hi Mark, GLU can't do forward variable selection automatically. It would not be difficult to add,
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forward stepwise regression
Hi Mark, GLU can't do forward variable selection automatically. It would not be difficult to add,
8/13/12
Mark
, …
Nicholas Orr
7
5/22/12
Ordered Polytomous Regression
Hi Mark, I think you can recode the ped file in PLINK using the --recode12 option Nick Nick Orr, PhD
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Ordered Polytomous Regression
Hi Mark, I think you can recode the ped file in PLINK using the --recode12 option Nick Nick Orr, PhD
5/22/12
Wagner Magalhaes
,
Kevin Jacobs <jacobs@bioinformed.com>
4
4/24/12
Fwd: glu problem
Hi Wagner, Illumina has only recently released hg19/GRCh37 versions of their chip manifest files in
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Fwd: glu problem
Hi Wagner, Illumina has only recently released hg19/GRCh37 versions of their chip manifest files in
4/24/12
INK
, …
Jacobs, Kevin (NIH/NCI) [C]
11
3/22/12
GLU crash
If anyone, I should be thanking you for the code and swift support! Igor On Mar 22, 4:12 pm, "
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GLU crash
If anyone, I should be thanking you for the code and swift support! Igor On Mar 22, 4:12 pm, "
3/22/12
Mark
,
Jacobs, Kevin (NIH/NCI) [C]
2
3/21/12
Removing SNPs in linkage -> ld.filter?
Hi Mark, I'm happy to help. The programs have evolved faster than the documentation. Here is how
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Removing SNPs in linkage -> ld.filter?
Hi Mark, I'm happy to help. The programs have evolved faster than the documentation. Here is how
3/21/12
Jacobs, Kevin (NIH/NCI) [C]
,
Mark
2
3/19/12
RE: Output of SE in assoc.logit1
Hi I am using the --se option in the assoc.logit1 module. While the output gives the OR and the --ci
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RE: Output of SE in assoc.logit1
Hi I am using the --se option in the assoc.logit1 module. While the output gives the OR and the --ci
3/19/12
Wagner Magalhães
, …
Nicholas Orr
5
1/24/12
ginfo error
Hi Kevin, Clearly 1-4 are all potentially troublesome if ignored. Option A is fine for studies with
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ginfo error
Hi Kevin, Clearly 1-4 are all potentially troublesome if ignored. Option A is fine for studies with
1/24/12
amontoya
,
Kevin Jacobs <jacobs@bioinformed.com>
2
8/16/11
32 bits binaries
Hi Adan, I don't even have access to a 32 bit Linux system anymore and haven't for years. I
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32 bits binaries
Hi Adan, I don't even have access to a 32 bit Linux system anymore and haven't for years. I
8/16/11
amontoya
8/16/11
32-bit linux binary
Is it possible to post 32 bit linux binaries?
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32-bit linux binary
Is it possible to post 32 bit linux binaries?
8/16/11
acpatel
,
Jacobs, Kevin (NIH/NCI) [C]
2
5/5/11
problem with Newbler2SAM
Hi Anand, I may be making some undue DNAseq assumptions about the SFF files. Could you send me a
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problem with Newbler2SAM
Hi Anand, I may be making some undue DNAseq assumptions about the SFF files. Could you send me a
5/5/11
jvanhan
,
Kevin Jacobs <jacobs@bioinformed.com>
2
3/9/11
modifying bpm files?
Hi Jack, GLU doesn't have a BPM writer, though it wouldn't be terribly difficult to build one
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modifying bpm files?
Hi Jack, GLU doesn't have a BPM writer, though it wouldn't be terribly difficult to build one
3/9/11
Jacobs, Kevin (NIH/NCI) [C]
3/2/11
GLU 1.0b2 pre-release binaries for Linux not available
I've posted Linux 64-bit binaries for a pre-release of GLU 1.0 beta 2 and updated genedb files,
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GLU 1.0b2 pre-release binaries for Linux not available
I've posted Linux 64-bit binaries for a pre-release of GLU 1.0 beta 2 and updated genedb files,
3/2/11
Faheem Mitha
, …
kowzar
7
2/28/11
does GLU use a database
Hi Kevin. I take it that the only way for the two systems (GLU and SNPpy) to interact would be
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does GLU use a database
Hi Kevin. I take it that the only way for the two systems (GLU and SNPpy) to interact would be
2/28/11
vincenzo moreschini
, …
Jacobs, Kevin (NIH/NCI) [C]
6
2/14/11
build error
Congratulations! Please let me know if you run into any trouble and I'll be happy to help. The
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build error
Congratulations! Please let me know if you run into any trouble and I'll be happy to help. The
2/14/11
vdesb...@immport.org
, …
Jacobs, Kevin (NIH/NCI) [C]
8
2/11/11
convert an Illumina manifest file (ex. - Human1M-Duov3_C.bpm) to a standard .csv file or tab-delimited file
Hi Kevin, Wow, that's great. Thanks for the information on the "altinstall" option. So
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convert an Illumina manifest file (ex. - Human1M-Duov3_C.bpm) to a standard .csv file or tab-delimited file
Hi Kevin, Wow, that's great. Thanks for the information on the "altinstall" option. So
2/11/11
Geert Vandeweyer
,
Kevin Jacobs <jacobs@bioinformed.com>
2
2/11/11
Using glu to convert illumina bpm files
Absolutely-- the modules.convert.dump_bpm does exactly that. -Kevin On Fri, Feb 11, 2011 at 5:38 AM,
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Using glu to convert illumina bpm files
Absolutely-- the modules.convert.dump_bpm does exactly that. -Kevin On Fri, Feb 11, 2011 at 5:38 AM,
2/11/11
FCicconardi
, …
Kevin Jacobs <jacobs@bioinformed.com>
10
2/9/11
seq.Newbler2SAM
Thank you very much! I'll give a try! F Francesco Cicconardi, Ph.D
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seq.Newbler2SAM
Thank you very much! I'll give a try! F Francesco Cicconardi, Ph.D
2/9/11
denis laloe
,
Kevin Jacobs <jacobs@bioinformed.com>
2
2/12/10
Tracy-Widom statistics
On Fri, Feb 12, 2010 at 9:38 AM, denis laloe <denis...@jouy.inra.fr> wrote: In the revision
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Tracy-Widom statistics
On Fri, Feb 12, 2010 at 9:38 AM, denis laloe <denis...@jouy.inra.fr> wrote: In the revision
2/12/10
Lee Watkins/Hopkins/CIDR
,
Kevin Jacobs <jacobs@bioinformed.com>
2
9/2/09
Any progress on OS X binary?
Hi Lee, I've produced several test versions for OS X (Intel) and apologize for not uploading them
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Any progress on OS X binary?
Hi Lee, I've produced several test versions for OS X (Intel) and apologize for not uploading them
9/2/09
Wagner Magalhães
, …
Jacobs, Kevin (NIH/NCI) [C]
5
8/31/09
genedb.find_snps module
Hi Wagner, You can obtain genedb from the LTG server by copying the following file to your local PC:
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genedb.find_snps module
Hi Wagner, You can obtain genedb from the LTG server by copying the following file to your local PC:
8/31/09
kowzar
, …
Jun
8
4/2/09
plink import
If GLU is installed locally, I believe one has to add that directory to the python path. Jun Lu On
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plink import
If GLU is installed locally, I believe one has to add that directory to the python path. Jun Lu On
4/2/09
Jacobs, Kevin (NIH/NCI) [C]
1/8/09
[ANNOUNCEMENT] GLU 1.0a6 Released
I am pleased to announce the release of GLU 1.0 alpha 6 (see below for a summary of changes). Source
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[ANNOUNCEMENT] GLU 1.0a6 Released
I am pleased to announce the release of GLU 1.0 alpha 6 (see below for a summary of changes). Source
1/8/09
Giordano_Souza
, …
Jacobs, Kevin (NIH/NCI) [C]
5
12/5/08
Trouble with HWE p value
I updated the documentation generation system to the latest version, regenerated the docs, and this
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Trouble with HWE p value
I updated the documentation generation system to the latest version, regenerated the docs, and this
12/5/08
Dtae
, …
Kevin Jacobs <jacobs@bioinformed.com>
11
11/23/08
glu - trouble with transform
Hello, > Good catch. I've corrected this. Please let me know if you notice any > other
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glu - trouble with transform
Hello, > Good catch. I've corrected this. Please let me know if you notice any > other
11/23/08