GIGSEA #720

zhushijia · 2018-04-10T21:14:55Z

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bioc-issue-bot · 2018-04-10T21:14:56Z

Hi @zhushijia

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: GIGSEA
Type: Package
Title: Genotype Imputed Gene Set Enrichment Analysis
Version: 0.99.0
Author: Shijia Zhu
Maintainer: Shijia Zhu <shijia.zhu@mssm.edu>
Description: We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method 
    that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set 
    enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, 
    e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, 
    SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as 
    weights both imputation accuracy and model completeness, was used to perform the enrichment test, 
    properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, 
    is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing 
    the computational intensive part in terms of large matrix operation. We have shown the appropriate type I 
    error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover 
    the real signal. 
License: LGPL-3
Encoding: UTF-8
LazyData: true
Depends: Matrix, MASS, locfdr, stats, utils
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
biocViews: GeneSetEnrichment,SNP,VariantAnnotation,GeneExpression,GeneRegulation,Regression,DifferentialExpression

bioc-issue-bot · 2018-04-10T22:59:30Z

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bioc-issue-bot · 2018-04-10T23:10:40Z

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bioc-issue-bot · 2018-04-11T11:39:11Z

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bioc-issue-bot · 2018-04-11T22:52:20Z

Received a valid push; starting a build. Commits are:

4ec2775 modification for bioconductor

bioc-issue-bot · 2018-04-11T23:12:47Z

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bioc-issue-bot · 2018-04-12T03:59:32Z

Received a valid push; starting a build. Commits are:

3a33da6 modification for bioconductor

bioc-issue-bot · 2018-04-12T04:09:11Z

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bioc-issue-bot · 2018-04-12T23:49:43Z

Received a valid push; starting a build. Commits are:

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bioc-issue-bot · 2018-04-13T00:01:31Z

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bioc-issue-bot · 2018-04-13T01:25:02Z

Received a valid push; starting a build. Commits are:

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bioc-issue-bot · 2018-04-13T01:36:27Z

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bioc-issue-bot · 2018-04-13T06:47:23Z

Received a valid push; starting a build. Commits are:

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bioc-issue-bot · 2018-04-13T06:56:42Z

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bioc-issue-bot · 2018-04-13T07:03:58Z

Received a valid push; starting a build. Commits are:

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bioc-issue-bot · 2018-04-13T07:16:54Z

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bioc-issue-bot · 2018-04-13T07:21:04Z

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bioc-issue-bot · 2018-05-29T05:49:45Z

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bioc-issue-bot · 2018-05-29T06:31:26Z

Received a valid push; starting a build. Commits are:

e4dddd0 4 space
e2a1372 4 space

bioc-issue-bot · 2018-05-29T06:59:14Z

Dear Package contributor,

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LiNk-NY · 2018-05-29T16:17:23Z

Hi ShiJia, @zhushijia

Please remove the .Rproj.user folder from the repository.
It seems like you accidentally deleted your .gitignore file and
commited files that were supposed to be ignored. Please re-add this file.

Your package is close to being accepted. Thank you.

Regards,
Marcel

bioc-issue-bot · 2018-05-30T05:40:23Z

Received a valid push; starting a build. Commits are:

5f8d0e0 rm .Rproj.user; add .gitignore; cat->message and v...
e57ed04 version

zhushijia · 2018-05-30T05:43:34Z

Hi LiNk-NY, @LiNk-NY

As suggested, I already removed the .Rproj.user folder, and added the .gitignore file.
Thank you very much for your patient help!

Best
Shijia

bioc-issue-bot · 2018-05-30T05:51:14Z

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS".
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bioc-issue-bot · 2018-05-30T06:11:41Z

Received a valid push; starting a build. Commits are:

84a855b version

bioc-issue-bot · 2018-05-30T06:20:54Z

Dear Package contributor,

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LiNk-NY · 2018-05-30T15:46:51Z

Hi ShiJia, @zhushijia
Thanks for making those changes.
Your package has been accepted.

Best regards,
Marcel

bioc-issue-bot · 2018-05-30T15:46:59Z

Your package has been accepted. It will be added to the
Bioconductor Git repository and nightly builds. Additional
information will be posed to this issue in the next several
days.

Thank you for contributing to Bioconductor!

mtmorgan · 2018-05-30T17:19:58Z

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/zhushijia.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using biocLite(\"GIGSEA\"). The package 'landing page' will be created at

https://bioconductor.org/packages/GIGSEA

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

zhushijia · 2018-05-31T01:49:27Z

Hi Martin, Yes, it has ssh public keys. Thank you very much for your help! Best Shijia

…

On Wed, May 30, 2018 at 1:20 PM, Martin Morgan ***@***.***> wrote: The master branch of your GitHub repository has been added to Bioconductor's git repository. To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/zhushijia.keys is not empty), then no further steps are required. Otherwise, do the following: 1. Add an SSH key to your github account <https://help.github.com/articles/connecting-to-github-with-ssh/> 2. Submit your SSH key to Bioconductor <https://git.bioconductor.org/BiocCredentials/> See further instructions at https://bioconductor.org/developers/how-to/git/ for working with this repository. See especially https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ to keep your GitHub and Bioconductor repositories in sync. Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at https://bioconductor.org/checkResults/ (Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using biocLite(\"GIGSEA\"). The package 'landing page' will be created at https://bioconductor.org/packages/GIGSEA If you have any questions, please contact the bioc-devel mailing list ( https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#720 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFKtsYXtY7DMdgyjoREM4cCntn1MpA0Kks5t3tTAgaJpZM4TPAoV> .

zhushijia · 2018-06-04T19:23:18Z

Hi Marcel, I would like to submit the corresponding experimental data for the GIGSEA package: https://github.com/zhushijia/GIGSEAdata But the submission of GIGSEA has been accepted, and the issue has been closed. So, may I ask whether I should open a new issue for the GIGSEAdata? Thank you very much! Best Shijia

…

On Wed, May 30, 2018 at 11:46 AM, Marcel Ramos ***@***.***> wrote: Hi ShiJia, @zhushijia <https://github.com/zhushijia> Thanks for making those changes. Your package has been accepted. Best regards, Marcel — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#720 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFKtseUjNVmmGng3ypxz9HpDb7xvL31_ks5t3r7ugaJpZM4TPAoV> .

zhushijia · 2018-06-06T20:24:25Z

Hi Martin, I would like to submit the corresponding experimental data for the GIGSEA package: https://github.com/zhushijia/GIGSEAdata But the submission of GIGSEA has been accepted, and the issue has been closed. So, may I ask whether I should open a new issue for the GIGSEAdata? Thank you very much! Best

…

On Wed, May 30, 2018 at 1:20 PM, Martin Morgan ***@***.***> wrote: Closed #720 <#720>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#720 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFKtsYXtY7DMdgyjoREM4cCntn1MpA0Kks5t3tTAgaJpZM4TPAoV> .

mtmorgan · 2018-06-06T20:31:07Z

Yes I suggest simply opening another issue.

LiNk-NY · 2018-06-06T20:31:13Z

Hi Shijia, @zhushijia
Sorry I missed your message.
It would've been better to submit both packages in one issue but now that the issue is closed,
please create another issue and submit it there.
Thanks!
Regards,
Marcel

zhushijia · 2018-06-06T20:35:15Z

Got it! Thank you very much, Martin.

…

On Wed, Jun 6, 2018 at 4:31 PM, Martin Morgan ***@***.***> wrote: Yes I suggest simply opening another issue. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#720 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFKtsceqEyH5MDL7wuGy7cW7zBVAdVIIks5t6DwNgaJpZM4TPAoV> .

zhushijia · 2018-06-06T20:36:35Z

Hi Marcel, no problem. Got it! Thank you very much! Best Shijia

…

On Wed, Jun 6, 2018 at 4:31 PM, Marcel Ramos ***@***.***> wrote: Hi Shijia, @zhushijia <https://github.com/zhushijia> Sorry I missed your message. It would've been better to submit both packages in one issue but now that the issue is closed. Please create another issue and submit it there. Thanks! Regards, Marcel — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#720 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFKtsR3FljaMa2VKEojNlDz87WH_8g92ks5t6DwSgaJpZM4TPAoV> .

bioc-issue-bot added the 1. awaiting moderation label Apr 10, 2018

bioc-issue-bot added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed 1. awaiting moderation labels Apr 10, 2018

bioc-issue-bot assigned LiNk-NY Apr 10, 2018

bioc-issue-bot added the ERROR label Apr 10, 2018

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bioc-issue-bot added the VERSION BUMP REQUIRED label Apr 12, 2018

bioc-issue-bot removed the VERSION BUMP REQUIRED label Apr 12, 2018

bioc-issue-bot removed the ERROR label Apr 13, 2018

bioc-issue-bot added the VERSION BUMP REQUIRED label Apr 13, 2018

bioc-issue-bot removed the VERSION BUMP REQUIRED label Apr 13, 2018

bioc-issue-bot added the ERROR label Apr 13, 2018

bioc-issue-bot removed the ERROR label Apr 13, 2018

bioc-issue-bot added OK and removed ERROR labels May 29, 2018

bioc-issue-bot added WARNINGS VERSION BUMP REQUIRED and removed OK labels May 30, 2018

bioc-issue-bot removed the VERSION BUMP REQUIRED label May 30, 2018

bioc-issue-bot added OK and removed WARNINGS labels May 30, 2018

LiNk-NY added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels May 30, 2018

mtmorgan closed this as completed May 30, 2018

GIGSEA #720

GIGSEA #720

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LiNk-NY commented Jun 6, 2018 • edited

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edited