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User: Fabian Grammes

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Posts by Fabian Grammes

<prev • 8 results • page 1 of 1 • next >
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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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GRangesList: wiered error
... 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 ...
genomicfeatures genomicranges written 15 months ago by Fabian Grammes • 20
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Comment: C: makeOrgPackage problems accessing RefSeq table
... 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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makeOrgPackage problems accessing RefSeq table
... 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 ...
annotationdbi written 2.3 years ago by Fabian Grammes • 20 • updated 2.3 years ago by James W. MacDonald ♦ 49k
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Answer: A: VariantAnnotation CollapsedVCF trouble
... 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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VariantAnnotation CollapsedVCF trouble
... 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 ...
variantannotation subsetting written 2.4 years ago by Fabian Grammes • 20
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DEXSeq: No log2FCs in DEXSeqResult table
... 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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Custom GeneSetCollection PFAM
... 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 ...
organism written 4.7 years ago by Fabian Grammes • 20 • updated 4.7 years ago by Martin Morgan ♦♦ 22k

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