Admin: shepherl

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shepherl ♦♦ 730
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Bioconductor Core Team Member

Posts by shepherl

<prev • 169 results • page 2 of 17 • next >
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Answer: A: annotationhub: data update
... We keep all records including old records for data reproducibility. As far as updating, We update bioconductor maintained resources every release - user contributed annotations we rely on the maintainers to submit proper updates. It would be impossible for us to regenerate user contributed resourc ...
written 5 weeks ago by shepherl ♦♦ 730
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Comment: C: ExperimentHub wackiness (which breaks packages that depend upon experimentHub-pr
... A few thoughts - install("sesameData", localHub=TRUE) is not a valid call. The localHub=TRUE argument is used in the ExperimentHub constructor not in install/install.packages. eh = ExperimentHub(localHub=TRUE). I just tried removing and installing the package install("sesameData") and I cannot repr ...
written 5 weeks ago by shepherl ♦♦ 730
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Comment: C: Installation of package 'FDb.InfiniumMethylation.hg19' fails
... If you set the `.libPaths()` is it possible that the org package got installed in a different path before you set it? Could you try reinstalling the org.Hs.eg.db after you set the .libPaths() to make sure it is in the same location. ...
written 5 weeks ago by shepherl ♦♦ 730
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News: List of Deprecated Packages for Bioc3.8
... 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 is as follows: Maintainer requested deprecation: Software: Go ...
news package release deprecate written 7 weeks ago by shepherl ♦♦ 730
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News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
... Hello all, The ensembl 93 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 1.30.1), ?BiocManager::install for help > library(AnnotationHub) > hub = AnnotationHub() snapshotD ...
annotationdata annotationhub news ensembl gtf 2bit written 7 weeks ago by shepherl ♦♦ 730
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Comment: C: Custom BSgenome with makeTxDbFromGFF
... I'll look into trying to clarify the ERROR message.    ...
written 7 weeks ago by shepherl ♦♦ 730
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Comment: C: Custom BSgenome with makeTxDbFromGFF
... I think you might still be able to use the Local BSgenomes but I think you would have to specify a taxonomyId.  The ERROR you are seeing is stemming from a lookup of the provided argument organism's taxonomyId - if the id is provided it skips this step.   ...
written 7 weeks ago by shepherl ♦♦ 730
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Comment: C: Custom BSgenome with makeTxDbFromGFF
... A few thoughts: You could update to use the latest version of R (3.5) and Bioconductor (3.7) You could utlize the available.species() function to see if the organism argument needs to be updated. Its possible we have tightened the constraint on the naming. Looking at the available.species( ...
written 7 weeks ago by shepherl ♦♦ 730
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Answer: A: getting mouse gene ids from makeTxDbFromUCSC()
... There are some annotation packages you can use like the TxDb.Mmusculus.UCSC.mm10.knownGene or Mus musculus package that already has the TxDb or OrgDb objects created. Perhaps something like the following is what you are looking for: library(Mus.musculus) genes(Mus.musculus, columns = c("ENTREZID" ...
written 7 weeks ago by shepherl ♦♦ 730
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Comment: C: Guidance to handle .CEL file in R
... You might consider reading through some of the Bioconductor workflows that would be appropriate for your data. Or searching the Bioconductor Software packages for key terms like 'affymetrix' or 'chip' and reading through the package vignette. ...
written 9 weeks ago by shepherl ♦♦ 730

Latest awards to shepherl

Scholar 6 weeks ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 3 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 15 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Appreciated 15 months ago, created a post with more than 5 votes. For DOI for packages
Centurion 15 months ago, created 100 posts.
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Bioconductor packages now each have a DOI.
Scholar 15 months ago, created an answer that has been accepted. For A: MSstats package update
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: survcomp package - censor missing
Scholar 2.4 years ago, created an answer that has been accepted. For A: survcomp package - censor missing

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