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User: Fabian Grammes
Fabian Grammes • 20
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Posts by Fabian Grammes
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Answer:
A: GRangesList: wiered error
... Thanks for the quick response Michael !
I agree that genomation should ideally accept txdb objects as input. Had to make a minor modification to make it work:
mcols(int) <- DataFrame("score" = as(rep(0, length(int)), "IntegerList"),
"name" = int$gene_id)
cheers, Fab ...
written 15 months ago by
Fabian Grammes • 20
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... Hi
I want to make a GRangesList containing exon,intron, promoter and TSS that I can subsequently use with the genomation::annotateWithGeneParts function. Should be easy, however when I try do that starting from a GenomicFeatures txdb package, extracting the parts I want and then try to make `GRang ...
written 15 months ago by
Fabian Grammes • 20
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... Thanks for the response James. I haven't started using AnnotationHub but clearly I should look more into it.
1. Both packages available from AnnotationHub are not up to date since they do not contain the results from the Salmo salar genome / transcriptome (published this summer), so I guess in that ...
written 2.3 years ago by
Fabian Grammes • 20
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... Dear All
I generated a an OrgDb package for Salmo salar, using `AnnotationForge::makeOrgPackage()`. However, the sqlite table REFSEQ (containing RefSeq IDs) is missing when I load the package
libarary(org.Ssalar.eg.db)
columns(org.Ssalar.eg.db)
[1] "ACCESSION" "CIGENE_ID" "GENENAME" "GE ...
written 2.3 years ago by
Fabian Grammes • 20
• updated
2.3 years ago by
James W. MacDonald ♦ 49k
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... Thanks that solves it ! Found two entries with 2 AF values. Really gave me a headache
...
written 2.4 years ago by
Fabian Grammes • 20
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... Dear All
I'm trying to access columns from the CollapsedVCF object generated by VariantAnnotation::readVcf. I have data for 3847 SNPs in the object, but when sub-setting I get 2 additional entries which I don't know where they come from. Looking at the CollapsedVCF object I can see that there seems ...
written 2.4 years ago by
Fabian Grammes • 20
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... Dear All
I have a Dataset with 3 conditions (2,3 and 4 replicates). I'm mainly
interested in the
exon expressions of one particular gene.
Looking at the DEXSeqResult table I noticed that NO log2FCs for all
exons of my gene
of interest where estimated. However, I do get a pvalue/adjpvalue for
most o ...
written 4.6 years ago by
Fabian Grammes • 20
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... Dear all
I'm working with an unsupported organism. However I have a table
of PFAM annotations for my genes and would like to make a
GeneSetCollection out of it (to use it later for hypergeometric
testing
etc...)
So how would I get a data set like this:
gene_id pfam_id
XLOC_000002 PF00354
XLOC_000 ...
written 4.7 years ago by
Fabian Grammes • 20
• updated
4.7 years ago by
Martin Morgan ♦♦ 22k
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