User: sandeep.amberkar18

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Posts by sandeep.amberkar18

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Comment: C: GO enrichment for non-model plant species
... No, I didn't create a GeneSetCollection object. How could that be passed to `enricher` function? ...
written 6 weeks ago by sandeep.amberkar180
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GO enrichment for non-model plant species
... Hello, Has anyone done an enrichment analysis for non-model plant species such as Wheat (Triticum aestivum). As a first step, I generated a gene-GO-GOdescription mapping as fetched from Ensembl Plants, which looks something like this: GeneID GO-ID ...
gseabase clusterprofiler gmtfiles written 6 weeks ago by sandeep.amberkar180
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Comment: C: DESeq2 nested effect with 5 variables
... Hi Michael, Sorry I should have explained the exp. design better, the full experiment consists of an expression dataset comprising: - 2 cultivars, each has - 2 tissues, sampled at - 2 temperatures, taken at - 2 time points, sampled at - 3 dev. stages, each having 4x replicates The metad ...
written 7 weeks ago by sandeep.amberkar180
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Comment: C: DESeq2 nested effect with 5 variables
... Hi Michael, Sorry I should have explained the exp. design better, the full experiment consists of an expression dataset comprising: - 2 cultivars, each has - 2 tissues, sampled at - 2 temperatures, taken at - 2 time points, sampled at - 3 dev. stages, each having 4x replicates The metad ...
written 7 weeks ago by sandeep.amberkar180
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DESeq2 nested effect with 5 variables
... Hello All, I'm dealing with a rather complex RNAseq experiment that follows a nested structure of the tested variables that could be represented like this: SampleName tissue temp time dev_stage rep Sample1 crown 21 am ds1 rep1 Sample2 crown 21 am ds1 rep3 Sample3 crown 21 am ds1 re ...
deseq2 rna-seq written 7 weeks ago by sandeep.amberkar180 • updated 7 weeks ago by Michael Love25k

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