Admin: shepherl

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shepherl ♦♦ 1.6k
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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 • 362 results • page 1 of 37 • next >
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Answer: A: Docker container with bioconductor and devtools
... Not directly as devtools isn't a Bioconductor package and isn't a requirement for Bioconductor packages. However we encourage you to look at the [bioconductor_full docker](https://github.com/Bioconductor/bioconductor_full) available via [dockerhub](https://cloud.docker.com/u/bioconductor/repositor ...
written 14 hours ago by shepherl ♦♦ 1.6k
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News: Important Deadlines for RELEASE
... Some Important Release Deadlines are fast approaching. See also the [release schedule online](http://bioconductor.org/developers/release-schedule/) The last day for any NEW package to be accepted and released under Bioc 3.10 is this **Wed. October 23th.** Packages accepted after this day will rem ...
news release devel deadline written 17 hours ago by shepherl ♦♦ 1.6k • updated 17 hours ago by Martin Morgan ♦♦ 23k
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Answer: A: Are AH52264, AH66175, and AH70594 duplicates?
... We rebuild the TxDb per release cycle to account for any changes; A new version but for the same genome build. The most recent will likely be what you want but we don't strictly replace so people could replicate older analysis. ...
written 3 days ago by shepherl ♦♦ 1.6k
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Answer: A: How to write the installation section in the vignette of a package that has not
... Yes you should ignore the fact that it is not on Bioconductor yet and include the above section. Keep in mind code like this, that shows installation, should be in a code chunk set with `eval=FALSE` so that it is not actually run (even when it is on officially on Bioconductor). If you are afraid ...
written 6 days ago by shepherl ♦♦ 1.6k
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News: Deadline for commits to current Release 3.9 Branch
... In preparation for the Bioconductor 3.10 release on October 30th we will be freezing the current release 3.9 branch on **Tuesday October 15th** . There will be no opportunities to commit or correct the release 3.9 branch after the freeze. We encourage everyone to push fixes as soon as possible an ...
news release deadline written 10 days ago by shepherl ♦♦ 1.6k
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Answer: A: Cannot Install Org.Hs.eg.db package in RStudio
... It looks like the file didn't download correctly. You could try the command again ``` BiocManager::install("org.Hs.eg.db") ``` If you continue to have trouble. You could download the tar.gz file to your computer and do a manual install of the package using ``` install.packages(, repos=NULL) ``` ...
written 12 days ago by shepherl ♦♦ 1.6k
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Answer: A: Final List of Deprecated Packages for Bioc3.10
... scone will be un-deprecated and remain in Bioconductor. ...
written 14 days ago by shepherl ♦♦ 1.6k
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News: Final List of Deprecated Packages for Bioc3.10
... 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 final list for this release is as follows: Maintainer requested deprecation: Software: SNPchip GenomeGraphs ...
annotation experimentdata news software release deprecation written 14 days ago by shepherl ♦♦ 1.6k
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News: Package Submission Deadline is TODAY!!
... The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.10 release is **TODAY** 5 PM EST! Please note: submission by this date does not guarantee it will be included - the package must undergo an official review and be a ...
news release package submission new submission deadline written 17 days ago by shepherl ♦♦ 1.6k
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News: Certificate ERROR resolved
... The certificates have been updated. Anyone that was having trouble accessing https://bioconductor.org should now be able. If any further troubles persist please let us know. (Sometimes clearing the browser cache is necessary to pick up the changes. There are some links in [this post](https://sup ...
news bioconductor website written 18 days ago by shepherl ♦♦ 1.6k

Latest awards to shepherl

Scholar 3 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Supporter 9 months ago, voted at least 25 times.
Appreciated 9 months ago, created a post with more than 5 votes. For Updated Support Site Editor
Scholar 9 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Autobiographer 9 months ago, has more than 80 characters in the information field of the user's profile.
Guru 10 months ago, received more than 100 upvotes.
Scholar 11 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 12 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Is there any annotation package for MSEA?
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
Scholar 16 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 2.4 years ago, created an answer that has been accepted. For A: survcomp package - censor missing
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: Bioconductor packages now each have a DOI.
Scholar 2.4 years ago, created an answer that has been accepted. For A: MSstats package update
Appreciated 2.4 years ago, created a post with more than 5 votes. For DOI for packages
Centurion 2.4 years ago, created 100 posts.
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: survcomp package - censor missing
Scholar 3.5 years ago, created an answer that has been accepted. For A: survcomp package - censor missing

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