Admin: shepherl

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shepherl ♦♦ 1.4k
Reputation:
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United States
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Joined:
3 years, 3 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 • 318 results • page 1 of 32 • next >
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Comment: C: OrgDB download failed via AnnotationHub
... Yes I will update. I removed the currently dataset from the database. The maintainer has regenerated the data and I am performing some checks now. I hope to have them uploaded by the end of the week but I will post back when they have been added back in. ...
written 4 days ago by shepherl ♦♦ 1.4k
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Comment: C: Can't install TopmedPipeline Package
... ``` install.packages("jomo") # if that is successful than try again: devtools::install_github("UW-GAC/analysispipeline/TopmedPipeline/") ``` ...
written 5 days ago by shepherl ♦♦ 1.4k
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Comment: C: Can't install TopmedPipeline Package
... try `devtools::install_github("UW-GAC/analysispipeline/TopmedPipeline/")` ...
written 5 days ago by shepherl ♦♦ 1.4k
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Answer: A: Can't install TopmedPipeline Package
... This support site is for Bioconductor maintained packages. TopmedPipeline is not a Bioconductor maintained package and you might have better luck on [StackOverflow](https://stackoverflow.com/) or [Biostars](https://www.biostars.org/). For What Its worth. It does not look like TopmedPipeline is ...
written 5 days ago by shepherl ♦♦ 1.4k
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Comment: C: R Version 3.6.1
... This ERROR is seen when you try `source("https://bioconductor.org/biocLite.R")` on an R version > 3.5 . The ERROR is correct. As of R version 3.5, the proper way to install Bioconductor packages is by using `BiocManager` as described on the referenced page `https://bioconductor.org/install`. ...
written 6 days ago by shepherl ♦♦ 1.4k
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Comment: C: OrgDB download failed via AnnotationHub
... The 2019-05-02 is correct for the release (3.9) version of Bioconductor and 2019-08-02 is correct for the devel (3.10) version of Bioconductor. The online version always shows devel while the R code does filtering and displays based on your running version. Resources associated with a different ...
written 6 days ago by shepherl ♦♦ 1.4k
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Answer: A: Help with installation of readat package
... You will have to reach out to CRAN. According to the landing page the package has been removed https://cran.r-project.org/web/packages/pathological/index.html You could go to the archive link on the above page to install the package manually but using install or install.packages will not work. ...
written 12 days ago by shepherl ♦♦ 1.4k
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Answer: C: Problem in installing maEndToEnd package
... The ERROR messages above are actually coming from `arrayQualityMetrics` package not being able to install. It looks like it actually has to do with system dependencies. From some other packages that were having similar issues the suggestion is to reinstall XQuartz at https://www.xquartz.org/ an ...
written 12 days ago by shepherl ♦♦ 1.4k
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Comment: C: Error while running normOffsets in diffhic
... On quick glance, it looks like the documentation might be misleading. while the documentation indeed shows ``` ...: Other arguments to be passed to 'calcNormFactors' for 'type="scaling"', or 'loessFit' for 'type="loess"'. ``` When I examine the code the extra arguments appear to be ...
written 13 days ago by shepherl ♦♦ 1.4k
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Comment: C: Problem in installing maEndToEnd package
... Could you try installing from Bioconductor ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") # If you want the development versions of packages: BiocManager::install(version='devel') BiocManager::install("maEndToEnd") ``` You could also check the in ...
written 13 days ago by shepherl ♦♦ 1.4k

Latest awards to shepherl

Scholar 4 weeks ago, created an answer that has been accepted. For A: survcomp package - censor missing
Supporter 7 months ago, voted at least 25 times.
Appreciated 7 months ago, created a post with more than 5 votes. For Updated Support Site Editor
Scholar 7 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.
Guru 8 months ago, received more than 100 upvotes.
Scholar 9 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 10 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Is there any annotation package for MSEA?
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
Scholar 14 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 2.2 years ago, created an answer that has been accepted. For A: survcomp package - censor missing
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Bioconductor packages now each have a DOI.
Scholar 2.2 years ago, created an answer that has been accepted. For A: MSstats package update
Appreciated 2.2 years ago, created a post with more than 5 votes. For DOI for packages
Centurion 2.2 years ago, created 100 posts.
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: survcomp package - censor missing
Scholar 3.3 years ago, created an answer that has been accepted. For A: survcomp package - censor missing

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