Admin: shepherl

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shepherl ♦♦ 890
Reputation:
890
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Trusted
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United States
Last seen:
2 days, 10 hours ago
Joined:
2 years, 7 months ago
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l************@roswellpark.org

Bioconductor Core Team Member

Posts by shepherl

<prev • 199 results • page 1 of 20 • next >
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Comment: C: how to retrieve gene id from topGO results
... You could look at the mapping objects in org.Hs.eg.db The org.Hs.egGO might be a useful.  ...
written 4 days ago by shepherl ♦♦ 890
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Comment: C: Obtain GRanges object by gene names
... 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? ...
written 4 days ago by shepherl ♦♦ 890
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Comment: C: Error: 'biocValid' is not an exported object from 'namespace:BiocManager'
... 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() ...
written 10 days ago by shepherl ♦♦ 890
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Answer: A: Error: 'biocValid' is not an exported object from 'namespace:BiocManager'
... BiocManager::valid() will be the same as BiocInstaller::BiocValid() ...
written 10 days ago by shepherl ♦♦ 890
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Comment: C: Ensembl plants at annotationHub?
... Let's further this discussion off the support site  ...
written 16 days ago by shepherl ♦♦ 890
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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 16 days ago by shepherl ♦♦ 890
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Comment: C: R failing to load genome files from EnsDb.Hsapiens.v86
... I'm still unable to reproduce this - Could you try reinstalling with BiocManager::install("EnsDb.Hsapiens.v86") ...
written 19 days ago by shepherl ♦♦ 890
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Comment: C: R failing to load genome files from EnsDb.Hsapiens.v86
... What is the output when you do library(EnsDb.Hsapiens.v86) ls('package:EnsDb.Hsapiens.v86') ...
written 19 days ago by shepherl ♦♦ 890
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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 19 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 26 days ago by shepherl ♦♦ 890

Latest awards to shepherl

Scholar 5 weeks ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 9 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?
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Scholar 18 months ago, created an answer that has been accepted. For A: MSstats package update
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Scholar 2.6 years ago, created an answer that has been accepted. For A: survcomp package - censor missing
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