Admin: shepherl

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shepherl ♦♦ 1.7k
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3 years, 7 months ago
Email:
l************@roswellpark.org

Bioconductor Core Team Member.

I work as a Bioconductor Core Team Member out of Roswell Park Comprehensive Cancer Center in Buffalo, NY.  I'm active in many areas of the project but notably maintain the Single Package Builder for new submissions, AWS resources, Bioconductor core docker images, the main Bioconductor website, and this support site.  While all members of the team offer support and maintenance of core package and core structures, I'm particularly more responsible for BiocCheck, BiocFileCache, and the Hubs (AnnotationHub, AnnotationHubData, ExperimentHub, ExperimentHubData). 

Posts by shepherl

<prev • 381 results • page 1 of 39 • next >
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Comment: C: RSS for new packages unavailable?
... Also There is also the new_package channel on the community-bioc slack channel https://bioc-community.herokuapp.com/ And you can see packages in review as our review process is completely transparent https://github.com/Bioconductor/Contributions/issues ...
written 2 days ago by shepherl ♦♦ 1.7k
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Comment: C: RSS for new packages unavailable?
... We will look into the RSS feed but new packages for each release are announced in each [release announcement](http://bioconductor.org/news/bioc_3_10_release/) as well ...
written 2 days ago by shepherl ♦♦ 1.7k
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Comment: C: EventPointer analysis error
... For future reference please tag the package name (ie. EventPointer) as a key. The package maintainers will be notified of a post when this happens. It will be hard for the maintainers to help without more information. Please show the exact lines of code you are trying to run along with your `se ...
written 10 days ago by shepherl ♦♦ 1.7k
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Comment: C: Error while installing RforMassSpectrometry
... I have notified the maintainers of the installation page that they may want to update https://github.com/rformassspectrometry/RforMassSpectrometry/issues/5 ...
written 10 days ago by shepherl ♦♦ 1.7k
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Answer: A: Error while installing RforMassSpectrometry
... BiocManager will only install package dependencies that are available on CRAN or Bioconductor. Other packages that are on github need to be installed explicitly ``` # depending on the ordering of dependencies the order may need to change BiocManager::install("rformassspectrometry/MsCoreUtils", " ...
written 10 days ago by shepherl ♦♦ 1.7k
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News: Single Package Builder for New Package Submissions
... Hello all, We will be updating the Single Package Builder to build on Bioc 3.11 and R 4.0 later today and tomorrow. You can expect some downtown and some periods of intermittent activity. We appreciate your patience while we make the transition. Thank you. ...
news release submission new package written 23 days ago by shepherl ♦♦ 1.7k
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Comment: C: how to choose annotation file in AnnotationHub web server
... May I ask what code you used to determine the differences? For instance when I grab the ENTREZID column I get 35257 for all three: ``` one = ah[["AH75915"]] two = ah[["AH75916"]] three = ah[["AH75917"]] > length(keys(one, keytype="ENTREZID")) [1] 35257 > length(keys(two, keytype="ENTREZID ...
written 25 days ago by shepherl ♦♦ 1.7k
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News: List of Deprecated Packages Bioc 3.11
... The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages for Bioc 3.11 is as follows: Maintainer requested deprecatio ...
annotation experimentdata news software release deprecation written 26 days ago by shepherl ♦♦ 1.7k
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Answer: A: Final List of Deprecated Packages for Bioc3.10
... MafDb.ESP6500SI.V2.SSA137.hs37d5 MafDb.EXP6500SI.V2.SSA137.GRCh38 have been deprecated in 3.10 and removed from 3.11. ...
written 26 days ago by shepherl ♦♦ 1.7k
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Answer: C: BiocManager::install() gives ERROR
... Firstly, I would check your `.libPaths( )` to make sure that you are indeed loading the library from your expected path locations as well as installing packages into the right designation. Bioconductor Versions are closely associated with R versions. Bioconductor version 3.8 is designed to work ...
written 4 weeks ago by shepherl ♦♦ 1.7k

Latest awards to shepherl

Scholar 5 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Supporter 11 months ago, voted at least 25 times.
Appreciated 11 months ago, created a post with more than 5 votes. For Updated Support Site Editor
Scholar 11 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.
Guru 12 months ago, received more than 100 upvotes.
Scholar 13 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 14 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Is there any annotation package for MSEA?
Scholar 15 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 16 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 18 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 2.5 years ago, created an answer that has been accepted. For A: survcomp package - censor missing
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Bioconductor packages now each have a DOI.
Scholar 2.5 years ago, created an answer that has been accepted. For A: MSstats package update
Appreciated 2.5 years ago, created a post with more than 5 votes. For DOI for packages
Centurion 2.5 years ago, created 100 posts.
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: survcomp package - censor missing
Scholar 3.6 years ago, created an answer that has been accepted. For A: survcomp package - censor missing

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