User: Bohdan Khomtchouk

Reputation:
10
Status:
New User
Location:
Stanford University
Website:
https://about.me/bohda...
Last seen:
2 years, 2 months ago
Joined:
3 years, 10 months ago
Email:
k************@gmail.com

https://about.me/bohdankhomtchouk

Posts by Bohdan Khomtchouk

<prev • 8 results • page 1 of 1 • next >
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GEOmetadb package is missing "Organism" metadata field in all GSE accession IDs
... Hello, I ran into a bug in GEOmetadb: ​ library(GEOmetadb) if(!file.exists('GEOmetadb.sqlite')) getSQLiteFile() con <- dbConnect(SQLite(),'GEOmetadb.sqlite') dbListFields(con,'gse') ##  [1] "ID"                   "title"              ##  [3] "gse"                  "status"             ##  [5] " ...
geometadb written 2.2 years ago by Bohdan Khomtchouk10 • updated 2.2 years ago by Vincent J. Carey, Jr.6.3k
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Tutorial: Using Subversion to update /devel branch of Bioconductor package
... Hello Everybody!   I recently wrote up a comprehensive "batteries included" recipe for R package developers and maintainers to easily update the development (/devel) branch of their Bioconductor packages smoothly and efficiently using Subversion.  Here's a step-by-step recipe from A-Z to make sure ...
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Comment: C: Properly assigning gene list objects in GOsummaries
... This is the error I now get: P.S.  Doesn't one need to also specify the organism prior to generating a word cloud (i.e., for the apriori GO enrichment analysis)?  Here, my gene list has an RGD entry, so is clearly rat, but how would the GOsummaries package know what organism you're working with a ...
written 2.4 years ago by Bohdan Khomtchouk10
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Properly assigning gene list objects in GOsummaries
... I'd like to use the GOsummaries package in a workflow that I'm building.  But I do not understand the rationale behind how the genes1 and genes2 vectors were constructed in the package vignette (page 2): https://bioconductor.org/packages/release/bioc/vignettes/GOsummaries/inst/doc/GOsummaries-basics ...
gosummaries written 2.4 years ago by Bohdan Khomtchouk10 • updated 2.4 years ago by Raivo Kolde50
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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 2.4 years ago by Bohdan Khomtchouk10
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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 2.4 years ago by Bohdan Khomtchouk10 • updated 2.4 years ago by Peter Langfelder2.3k
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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 2.4 years ago by Bohdan Khomtchouk10 • updated 2.4 years ago by James W. MacDonald52k
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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 3.9 years ago by Bohdan Khomtchouk10

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For goseq: Can't find mm10/geneSymbol length data in genLenDataBase...

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