User: kirannbishwa01

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Posts by kirannbishwa01

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enrichGO from DOSE, clusterprofiler is returning empty result.
... I am trying to use enrichGO function from clusterProfiler package. All is good except that my results are empty. # for significant genes > sig.foldChangesAbv2 %>% length() [1] 244 > sig.foldChanges %>% head(5) [1] "NA1"       "AT1G64640" "AT1G64630" "AT1G64625" "NA3" # for universal ...
annotation clusterprofiler dose gene ontology gene set enrichment written 12 months ago by kirannbishwa01 • 0 • updated 12 months ago by Guangchuang Yu • 1.1k
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How to name the custom genome in karyoploteR ?
... I really like the features that are provided in karyoploteR. https://bioconductor.org/packages/release/bioc/html/karyoploteR.html But, I am working with different organisms. I am able to find the organisms of interest using: > available.genomes()  [1] "BSgenome.Alyrata.JGI.v1"                 ...
bsgenome software error R karyoploter written 12 months ago by kirannbishwa01 • 0 • updated 12 months ago by bernatgel • 90
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Comment: C: Add new columns to DESeqResults from text file by matching rownames.
... Hi Steve, I knew about this method, but the problem is that if you convert the S4-object using as.data.frame you are loosing valuable metadata information that are used downstream in the workflow. Any other ideas.   ...
written 13 months ago by kirannbishwa01 • 0
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Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
... HI Michael, If your time allows, Can you please look into this problem? https://support.bioconductor.org/p/101008/ ...
written 13 months ago by kirannbishwa01 • 0
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Add new columns to DESeqResults from text file by matching rownames.
... I have generated results from DESeq2 wihch is a S4 type R-object. I want to add new columns to it containing geneNames, contig and start position. There is method using BioMart to do it, but I won't be using the BioMart method; instead I have the geneDatabase as a textfile, I have tried merging th ...
deseq deseq2 s4vectors cbind merge data frames written 13 months ago by kirannbishwa01 • 0 • updated 13 months ago by Michael Love ♦ 20k
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Comment: C: Using edgeR or DESeq2 to analyze allele-specific expression?
... HI @Aaron: What do you mean by, "Dropping it will test for allele-specific expression, averaged across all individuals"? Are we not supposed to keep the design as it is as ~0+individual+allele   ...
written 13 months ago by kirannbishwa01 • 0

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