User: kmuench

gravatar for kmuench
kmuench30
Reputation:
30
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New User
Location:
United States
Last seen:
6 months ago
Joined:
2 years, 5 months ago
Email:
k******@stanford.edu

Posts by kmuench

<prev • 5 results • page 1 of 1 • next >
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What does this error mean? - issue implementing SVA
... Hello, I'm attempting to implement sva on my RNA-Seq count data matrix. I have a table, myFactors, which describes various potential sources of known (e.g., myFactors$Condition - control, condition1, condition2) and suspected (e.g., myFactors$Date - date of sample preparation) variation. I've foll ...
sva rna-seq written 2.2 years ago by kmuench30 • updated 20 days ago by Sandip Darji0
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Comment: C: Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
... Haha! Thank you for pointing that out! ...
written 2.4 years ago by kmuench30
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Comment: C: Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
... For posterity: my issue is specifically that the library doesn't seem to be available yet for my version of R (error: "package ‘ensembldb’ is not available (for R version 3.1.2)"). Currently working through these possibilities: http://stackoverflow.com/questions/25721884/how-should-i-deal-with-packa ...
written 2.4 years ago by kmuench30
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Comment: C: Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
... Thank you for the suggestion! I'm having trouble with the install (getting a "there is no package called ‘EnsDb.Hsapiens.v75’" message) but this looks like what I want - I'll keep trying. ...
written 2.4 years ago by kmuench30
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Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
... Hello, In R, I previously used this piece of code to look up Ensembl IDs for lists of genes beginning with ENSG000... .  In this example, my_df is a dataframe where the rownames are the gene IDs 9e.g. ENSG...):   my_df$ensembl <- sapply( strsplit( rownames(my_df), split="\\+" ), "[", 1 ) ...
rnaseq biomart R written 2.4 years ago by kmuench30 • updated 2.4 years ago by Johannes Rainer1.3k

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