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Admin: shepherl

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shepherl ♦♦ 1.1k
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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 • 223 results • page 1 of 23 • next >
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News: List of Deprecated Package Bioc 3.9
... 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 3.9 is as follows: Maintainer requested deprecatio ...
experimentdata news software release devel deprecate written 3 hours ago by shepherl ♦♦ 1.1k
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Comment: C: My post stopped getting sent via email
... While we did some major updates to the website a few weeks ago it should not have affected the email. I will look further into this. If it continues to be a problem please also open an issue at https://github.com/Bioconductor/support.bioconductor.org ...
written 8 hours ago by shepherl ♦♦ 1.1k
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News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
... We apologize for the delay: The ensembl 95 gtf (converted to GRanges on the fly) and fasta (twobit files) been added to AnnotationHub and are currently available in Bioc 3.9 ``` Bioconductor version 3.9 (BiocManager 1.30.4), ?BiocManager::install for help > hub = AnnotationHub() snapshotDate(): ...
annotationdata annotationhub news ensembl gtf 2bit written 7 days ago by shepherl ♦♦ 1.1k
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Comment: C: find proteomic dataset
... You can search the existing Bioconductor [Experiment Data Package](http://bioconductor.org/packages/release/BiocViews.html#___ExperimentData) to see if there are any packages that look like it would be promising. There are also two [proteomic workflows](http://bioconductor.org/packages/release/Bio ...
written 15 days ago by shepherl ♦♦ 1.1k
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Tutorial: Updated Support Site Editor
... You may have noticed in a recent round of updates to the support site, there is a new editor for posting. The default editor now uses markdown by default rather than being a plain text editor. You can still type as normal but there are some key features to be aware of with markdown. Some cheat shee ...
tutorial support.bioconductor.org markdown editor updates written 23 days ago by shepherl ♦♦ 1.1k
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Comment: C: Dealing with HSP in blast output with GRanges
... When I tried your above code I end up with something like the following: ``` > reduce(genes) GRanges object with 8 ranges and 0 metadata columns: seqnames ranges strand [1] scaffold_1 20-50 + [2] scaffold_1 130-300 + [3] scaffold_1 906-12 ...
written 4 weeks ago by shepherl ♦♦ 1.1k
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Comment: C: Identify Core packages
... Not really sure - The list of packages that are provided with the "core" docker container can be found at the bottom of the following [page](http://bioconductor.org/help/docker/). ...
written 4 weeks ago by shepherl ♦♦ 1.1k
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Comment: C: List of Deprecated Package Bioc 3.9
... chipseq will not be deprecated and has been fixed. ...
written 4 weeks ago by shepherl ♦♦ 1.1k
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Comment: C: Request to create an organism package
... We provide some species information automatically in annotationhub and then rely on user community contributed resources for any additional data. Some recommendations we have given for creating contributed annotation resources in the past For an OrgDb object, see makeOrgPackageFromNCBI() and m ...
written 5 weeks ago by shepherl ♦♦ 1.1k
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Comment: C: Ensembl 95 has been released
... When a new version of ensembl is release, Bioconductor generates annotation resources to provide to our users through our annotationhub based on the new version. I've done this many times for many versions. It appears there is some difficulty generating the resources based on the latest ensembl 95 ...
written 5 weeks ago by shepherl ♦♦ 1.1k

Latest awards to shepherl

Autobiographer 6 weeks ago, has more than 80 characters in the information field of the user's profile.
Guru 11 weeks ago, received more than 100 upvotes.
Scholar 3 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 4 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 5 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Is there any annotation package for MSEA?
Scholar 6 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 8 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 20 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Appreciated 20 months ago, created a post with more than 5 votes. For DOI for packages
Centurion 20 months ago, created 100 posts.
Scholar 20 months ago, created an answer that has been accepted. For A: MSstats package update
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Bioconductor packages now each have a DOI.
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: survcomp package - censor missing
Scholar 2.8 years ago, created an answer that has been accepted. For A: survcomp package - censor missing

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