PheWeb-UMich

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Jordi Valls, Sarah Gagliano Taliun2

Dec 12

Where is the raw data of UKBB-TOPmed

Thank you for your interest in PheWeb. On the TOPMed-imputed UKBB PheWeb, the full summary statistics

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Where is the raw data of UKBB-TOPmed

Thank you for your interest in PheWeb. On the TOPMed-imputed UKBB PheWeb, the full summary statistics

Dec 12

Eleanor Wheeler2

Aug 6

Internal Server Error

Seems to be working again now, thank you! On Wednesday 31 July 2024 at 12:36:12 UTC+1 Eleanor Wheeler

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Internal Server Error

Seems to be working again now, thank you! On Wednesday 31 July 2024 at 12:36:12 UTC+1 Eleanor Wheeler

Aug 6

Aug 4

Custom Search Route

I should also add that I added the custom_templates dirn to the config file, should clear any

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Custom Search Route

I should also add that I added the custom_templates dirn to the config file, should clear any

Aug 4

Ekin Yaman, … Sarah Gagliano Taliun3

Jul 29

Genome Build Used in the UK TopMed Imputed Biobank

Hello Ekin, Thanks for your interest in PheWeb. The TOPMed-imputed UK Biobank PheWeb is on GRCh38.

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Genome Build Used in the UK TopMed Imputed Biobank

Hello Ekin, Thanks for your interest in PheWeb. The TOPMed-imputed UK Biobank PheWeb is on GRCh38.

Jul 29

Shicheng Guo, Sarah Gagliano Taliun2

Jun 11

Cholesterol, LDL, HDL are not included in the analysis?

Copying and pasting my response to the Google Group, in case it is helpful to others: In this PheWeb

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Cholesterol, LDL, HDL are not included in the analysis?

Copying and pasting my response to the Google Group, in case it is helpful to others: In this PheWeb

Jun 11

Afreen Naz, Peter VandeHaar2

May 31

Clumping < 0.01

Pheweb does not do LD clumping. Pheweb does distance clumping in two places: the table below the

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Clumping < 0.01

Pheweb does not do LD clumping. Pheweb does distance clumping in two places: the table below the

May 31

Yura Lee, Peter VandeHaar2

Feb 13

The meaning of the symbols and how to download the phenotype summary?

The circles are associations where beta is near zero. I believe it's where abs(beta/sebeta) <

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The meaning of the symbols and how to download the phenotype summary?

The circles are associations where beta is near zero. I believe it's where abs(beta/sebeta) <

Feb 13

ping xu, Peter VandeHaar2

Feb 1

Hi Ping, I don't maintain pheweb anymore, but I know that this issue happens because the version

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Hi Ping, I don't maintain pheweb anymore, but I know that this issue happens because the version

Feb 1

Wynne, Peter VandeHaar2

7/19/23

Hi Wynne, Yeah, you could add that. You want to add 3 more pages like the phenotypes page, but each

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Hi Wynne, Yeah, you could add that. You want to add 3 more pages like the phenotypes page, but each

7/19/23

Wynne, Peter VandeHaar2

6/9/23

Speed up "Pheweb Process" step

Without any more details, I can only recommend more cpu cores and faster storage. You can also run on

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Speed up "Pheweb Process" step

Without any more details, I can only recommend more cpu cores and faster storage. You can also run on

6/9/23

4/7/23

LD highlighting not working?

I'm just using pheweb for the first time (nice tool!) and everything's pretty much gone great

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LD highlighting not working?

I'm just using pheweb for the first time (nice tool!) and everything's pretty much gone great

4/7/23

4/7/23

GWAS is performed using logistic regression

Dear all, We are interested in "290: Delirium dementia and amnestic and other cognitive

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GWAS is performed using logistic regression

Dear all, We are interested in "290: Delirium dementia and amnestic and other cognitive

4/7/23

Matthew Maher, … Andy Boughton4

4/5/23

LD highlighting

It's worth noting that LocusZoom matches LD information based on chrom/pos/ref/alt, not rsID. The

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LD highlighting

It's worth noting that LocusZoom matches LD information based on chrom/pos/ref/alt, not rsID. The

4/5/23

11/11/22

Missing data for some tissues

Hello, One of our variants that should be showing up for all tissues only shows up for two in the

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Missing data for some tissues

Hello, One of our variants that should be showing up for all tissues only shows up for two in the

11/11/22

Suchen Zheng, Sarah Gagliano Taliun2

10/31/22

Where to download all the summary statistic files?

wget should work! Le lundi 31 octobre 2022 à 15:38:12 UTC-4, sz...@yale.edu a écrit : Hello, If there

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Where to download all the summary statistic files?

wget should work! Le lundi 31 octobre 2022 à 15:38:12 UTC-4, sz...@yale.edu a écrit : Hello, If there

10/31/22

Charlie Repaci, Peter VandeHaar2

7/28/22

Huh, curious. What version of pheweb are you using? What did you set for “hg_build_number“ in config.

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Huh, curious. What version of pheweb are you using? What did you set for “hg_build_number“ in config.

7/28/22

Joseph Chase, Peter VandeHaar2

7/28/22

Specs on what this should take to run?

How many variants? How many phenotypes? I recommend loading on a big machine (50+ cores) or a cluster

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Specs on what this should take to run?

How many variants? How many phenotypes? I recommend loading on a big machine (50+ cores) or a cluster

7/28/22

Charlie Repaci2

6/9/22

Error in QQ plots

I've figured out the issue! My teammate passed me a small subset of the data to work with which

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Error in QQ plots

I've figured out the issue! My teammate passed me a small subset of the data to work with which

6/9/22

Jennifer Huffman, pjvandehaar2

10/3/21

effect allele when creating your own instance of PheWeb

Hi Jenny, PheWeb assumes that all of those are for the alternate allele. Thanks, I just updated the

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effect allele when creating your own instance of PheWeb

Hi Jenny, PheWeb assumes that all of those are for the alternate allele. Thanks, I just updated the

10/3/21

Mokerina Liao, Peter VandeHaar2

8/4/21

how to generate/input phewas data

You need one file for each phenotype (ie, one file per GWAS). Section 3 of the instructions describes

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how to generate/input phewas data

You need one file for each phenotype (ie, one file per GWAS). Section 3 of the instructions describes

8/4/21

Shicheng Guo, Peter VandeHaar2

7/14/21

Github web page

The Manhattan plot pages have a download link. See the top-right of https://pheweb.org/UKB-TOPMed/

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Github web page

The Manhattan plot pages have a download link. See the top-right of https://pheweb.org/UKB-TOPMed/

7/14/21

Shicheng Guo, Sarah Gagliano Taliun2

7/9/21

Pheweb data download - summary statistics

Hi! Thanks for your interest in PheWeb. Below are the locations to download summary statistics for

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Pheweb data download - summary statistics

Hi! Thanks for your interest in PheWeb. Below are the locations to download summary statistics for

7/9/21

Michael Chong, pjvandehaar2

6/19/21

Login Access outside of Google Accounts?

Here are options I can think of: 1. Your users can make google accounts connected to their non-google

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Login Access outside of Google Accounts?

Here are options I can think of: 1. Your users can make google accounts connected to their non-google

6/19/21

James Pirruccello, pjvh2

3/10/21

Effect allele vs minor allele vs non-reference allele in PheWeb

Yeah, it sounds like you figured everything out correctly. You're right that for a variant "

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Effect allele vs minor allele vs non-reference allele in PheWeb

Yeah, it sounds like you figured everything out correctly. You're right that for a variant "

3/10/21

James Warren, Peter VandeHaar4

2/19/21

upper bound on # of phenotypes?

Fantastic - thank you so much! On Friday, February 19, 2021 at 11:09:32 AM UTC-8 pjvh wrote: I added

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upper bound on # of phenotypes?

Fantastic - thank you so much! On Friday, February 19, 2021 at 11:09:32 AM UTC-8 pjvh wrote: I added

2/19/21

Fedik Rahimov, Peter VandeHaar2

2/10/21

R code for PheWEB

I'm glad you like how pheweb's manhattan plots work! Unfortunately, I don't have any

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R code for PheWEB

I'm glad you like how pheweb's manhattan plots work! Unfortunately, I don't have any

2/10/21

Ashley Qin, pjvandehaar2

2/2/21

Speed up "gather-pvalues-for-each-gene"

Sorry about getting back to you so late. Presumably you've figured it out by now. Yeah, that step

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Speed up "gather-pvalues-for-each-gene"

Sorry about getting back to you so late. Presumably you've figured it out by now. Yeah, that step

2/2/21

Pete Santos, Peter VandeHaar2

8/21/20

Having difficult getting started / following the README does not seem to work

It looks like that was failing because there were no significant associations in that tiny test file,

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Having difficult getting started / following the README does not seem to work

It looks like that was failing because there were no significant associations in that tiny test file,

8/21/20

Sarah Gagliano Taliun

8/18/20

Hello. This group is for discussion of PheWeb. GitHub: https://github.com/statgen/pheweb Citation:

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Hello. This group is for discussion of PheWeb. GitHub: https://github.com/statgen/pheweb Citation:

8/18/20

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