Admin: shepherl

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shepherl ♦♦ 650
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Posts by shepherl

<prev • 160 results • page 1 of 16 • next >
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Comment: C: annotationhub: data update
... Looking at the recipes in AnnotationHubData I do not see anything for RefSeq data which leads me to believe that it is not a core provided resource. I can investigate more into this and will bring it up at the core meeting later today. ...
written 21 hours ago by shepherl ♦♦ 650
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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 22 hours ago by shepherl ♦♦ 650
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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 3 days ago by shepherl ♦♦ 650
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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 3 days ago by shepherl ♦♦ 650
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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 13 days ago by shepherl ♦♦ 650
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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 15 days ago by shepherl ♦♦ 650
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Comment: C: Custom BSgenome with makeTxDbFromGFF
... I'll look into trying to clarify the ERROR message.    ...
written 17 days ago by shepherl ♦♦ 650
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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 17 days ago by shepherl ♦♦ 650
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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 17 days ago by shepherl ♦♦ 650
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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 17 days ago by shepherl ♦♦ 650

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