User: kirannbishwa01
kirannbishwa01 • 0
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Posts by kirannbishwa01
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... 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 ...
written 16 months ago by
kirannbishwa01 • 0
• updated
16 months ago by
Guangchuang Yu • 1.1k
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... 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" ...
written 16 months ago by
kirannbishwa01 • 0
• updated
16 months ago by
bernatgel • 90
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... 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 17 months ago by
kirannbishwa01 • 0
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... HI Michael,
If your time allows, Can you please look into this problem? https://support.bioconductor.org/p/101008/
...
written 17 months ago by
kirannbishwa01 • 0
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... 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 ...
written 17 months ago by
kirannbishwa01 • 0
• updated
17 months ago by
Michael Love ♦ 22k
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... 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 18 months ago by
kirannbishwa01 • 0
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