Admin: shepherl

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shepherl ♦♦ 890
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Bioconductor Core Team Member

Posts by shepherl

<prev • 201 results • page 2 of 21 • next >
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Comment: C: R failing to load genome files from EnsDb.Hsapiens.v86
... Could you please provide the code you are using and any output. Also please provide sessionInfo() so we know which version of R/Bioc and OS you are using. I currently can do the following with no error: > library(EnsDb.Hsapiens.v86) > db = EnsDb.Hsapiens.v86 > db EnsDb for Ensembl: |Ba ...
written 27 days ago by shepherl ♦♦ 890
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Comment: C: masigpro: could not find function "negative.binomial"
... It looks like that function is from the MASS package. You could loading the MASS library before running. library(MASS) > negative.binomial(10) Family: Negative Binomial(10) Link function: log ...
written 4 weeks ago by shepherl ♦♦ 890
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Answer: A: Cannot install Bioconductor Packages. Cannot install BiocManager.
... Please note we now have an updated install page that has a section for Legacy and Older versions of R. We still would always recommend updating to the latest version of R and packages but if this is not possible the installation instructions are now available. ...
written 4 weeks ago by shepherl ♦♦ 890
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Comment: C: How to monitor the performance of MS-based omics data?
... Consider also searching for omics in the biocViews search box with any other key terms to get a potential list of packages http://bioconductor.org/packages/release/BiocViews.html#___Software   Also consider proteomic workflows: http://bioconductor.org/packages/release/BiocViews.html#___Proteomic ...
written 5 weeks ago by shepherl ♦♦ 890
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Comment: C: problems regarding installing TEQC package
... The Error seems to suggest that you did not have internet connection at the time you tried this function. Can you ensure that you are connected to the internet and try again? Could you also include your sessionInfo() if you continue to have errors after checking the internet connection. ...
written 5 weeks ago by shepherl ♦♦ 890
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News: Initial 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 ...
news package release deprecate written 6 weeks ago by shepherl ♦♦ 890 • updated 6 weeks ago by Wolfgang Huber13k
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Comment: C: Recommended way to use BiocInstaller / BiocManager in packages on CRAN?
... BiocInstaller will still be available for older versions of R but will be defunct as of Bioconductor 3.9 (compatible with R 3.6.0).   BiocInstaller and BiocManager both manage package versions similarly, ensuring that the version of the packages being used are compatible with the version of R and Bi ...
written 6 weeks ago by shepherl ♦♦ 890
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Answer: A: dmrseq installation failed
... bumphumper has yet to build cleanly after the Bioconductor 3.8 release as indicated on the build report. Until the package builds it will be unavailable for installations. Once the package builds it will be available via BiocManager A temporary work around could be to either clone and install manua ...
written 6 weeks ago by shepherl ♦♦ 890
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Answer: A: GenomicFeatures won't install for 3.8 release
... Depending on what OS you are using, GenomicFeatures has a TIMEOUT on linux and ERROR on windows as indicated by the build report. Until there is a successful build on that platform it will remain unavailable. We are looking into these build failures. ...
written 6 weeks ago by shepherl ♦♦ 890
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News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
... Hello all, The ensembl 94 gtf (converted to GRanges on the fly) and fasta (twobit files) been added to AnnotationHub and are currently available in Bioc 3.8 Bioconductor version 3.8 (BiocManager 1.30.3), ?BiocManager::install for help > library(AnnotationHub) > hub = AnnotationHub() |==== ...
annotationdata annotationhub news ensembl gtf 2bit written 8 weeks ago by shepherl ♦♦ 890

Latest awards to shepherl

Scholar 6 weeks ago, created an answer that has been accepted. For A: survcomp package - censor missing
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Scholar 3 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Is there any annotation package for MSEA?
Scholar 4 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
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Scholar 18 months ago, created an answer that has been accepted. For A: MSstats package update
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