User: Bohdan Khomtchouk

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Stanford University
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Posts by Bohdan Khomtchouk

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Comment: C: org.Rn,eg.db not yet available for R version 3.3.3
... Oops, didn't notice the comma in: https://support.bioconductor.org/p/98138/#98185.  Thanks for the catch! ...
written 7 days ago by Bohdan Khomtchouk0
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org.Rn,eg.db not yet available for R version 3.3.3
... Hello, it looks like org.Rn,eg.db (and others like it) are not yet available for R version 3.3.3: > biocLite("org.Rn,eg.db") BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.3 (2017-03-06). Installing package(s) ‘org.Rn,eg.db’ Warning message: package ‘ ...
R package installation written 7 days ago by Bohdan Khomtchouk0 • updated 7 days ago by Peter Langfelder1.2k
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Returning gene functional annotations with gene symbols as input (using mygene Bioconductor package)
... I'm working with the following R code where I'm returning gene ontology terms pertinent to the biological process (BP) category: > source("https://bioconductor.org/biocLite.R") > biocLite("mygene") > xli <- c('BRCA1', 'BRCA2', 'SOX2', 'MYC') > res <- queryMany(xli ...
gene ontology software error R mygene written 9 days ago by Bohdan Khomtchouk0 • updated 7 days ago by James W. MacDonald43k
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goseq: Can't find mm10/geneSymbol length data in genLenDataBase...
... Has anyone else encountered any issues with using mm10 in the goseq package: > pwf <- nullp(genes, "mm10", "geneSymbol") Can't find mm10/geneSymbol length data in genLenDataBase... Found the annotaion package, TxDb.Mmusculus.UCSC.mm10.knownGene Trying to get the gene lengths from it. War ...
goseq written 18 months ago by Bohdan Khomtchouk0

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