Admin: shepherl
shepherl ♦♦ 890
- Reputation:
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Bioconductor Core Team Member
Posts by shepherl
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... It seems to suggest you are missing the dependency package "readr". Please try BiocManager::install("readr")
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written 5 days ago by
shepherl ♦♦ 890
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Answer:
A: Add TRF in mouse BSgenome
... There are two different BSgenome packages for mm10, BSgenome.Mmusculus.UCSC.mm10.masked and BSgenome.Mmusculus.UCSC.mm10. Doesn't the BSgenome.Mmusculus.UCSC.mm10.masked have the information you are looking for?
...
written 5 days ago by
shepherl ♦♦ 890
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... You could look at the mapping objects in org.Hs.eg.db The org.Hs.egGO might be a useful.
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written 14 days ago by
shepherl ♦♦ 890
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... I'm uncertain of your question? For clarification do you already have the genomic information for the desired genes or this is what you want to find out?
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written 14 days ago by
shepherl ♦♦ 890
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... biocValid() was a function in BiocInstaller which is deprecated. BiocManager has the function valid() to use. Please run BiocManager::valid() in place of running BiocInstaller::biocValid()
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written 20 days ago by
shepherl ♦♦ 890
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... BiocManager::valid() will be the same as BiocInstaller::BiocValid()
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written 20 days ago by
shepherl ♦♦ 890
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82
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Comment:
C: Ensembl plants at annotationHub?
... Let's further this discussion off the support site
...
written 26 days ago by
shepherl ♦♦ 890
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1
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Comment:
C: Ensembl plants at annotationHub?
... Also don't know if its helpful but there is a recent orgDb added to AnnotationHub for Arabidopsis matching the taxonomyid on the reference page you listed
> ah[which(mcols(ah)$taxonomyid==3702)]
AnnotationHub with 5 records
# snapshotDate(): 2018-11-01
# $dataprovider: UCSC, Inparanoid8, ftp:/ ...
written 26 days ago by
shepherl ♦♦ 890
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108
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... I'm still unable to reproduce this - Could you try reinstalling with
BiocManager::install("EnsDb.Hsapiens.v86")
...
written 29 days ago by
shepherl ♦♦ 890
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... What is the output when you do
library(EnsDb.Hsapiens.v86)
ls('package:EnsDb.Hsapiens.v86')
...
written 29 days 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
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
Scholar
11 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
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
Scholar
6 months ago,
created an answer that has been accepted.
For A: survcomp package - censor missing
Popular Question
6 months ago,
created a question with more than 1,000 views.
For BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
Scholar
18 months ago,
created an answer that has been accepted.
For A: survcomp package - censor missing
Centurion
18 months ago,
created 100 posts.
Commentator
18 months ago,
created a comment with at least 3 up-votes.
For C: Bioconductor packages now each have a DOI.
Scholar
2.6 years ago,
created an answer that has been accepted.
For A: survcomp package - censor missing
Teacher
2.6 years ago,
created an answer with at least 3 up-votes.
For A: survcomp package - censor missing
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