User: annamariabugaj
annamariabugaj • 0
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Posts by annamariabugaj
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I encountered a problem while performing analysis using the PANTHER website. I run the statistical overrepresentation test for a genelist of 99 genes (GO-Slim BP, Binomial, Bonferroni) in February 2020. My result was Bonferroni count = 1 and a list of several enriched GO terms. Next we run the s ...
written 5 months ago by
annamariabugaj • 0
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... yeah, I know - the problem is I came after the experiments were performed and I am asked to analyse the data... So I am just trying to do it the best way possible. ...
written 7 months ago by
annamariabugaj • 0
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... Thank you!
I have another question - I realised that I can actually split LEARN condition in two different conditions - NEW_room and FAMILIAR-room. In this case could I remove batch effect easier? Llike ~batch+condition?
I would have:
WT_BASE-batch1
WT_NEW_batch2
WT_FAMILIAR_batch2
I was also ...
written 7 months ago by
annamariabugaj • 0
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... Hello!
Please tell me if my reasoning is correct and how can I do run the proper analysis using DESEq2.
I have two batches of RNA-Seq samples: (format: TYPE_condition_batch)
WT_BASE_batch1
KO_BASE_batch1
WT_LEARN_batch2
KO_LEARN_batch2
I need to run DGE for WT_BASE and WT_LEARN and I don't ...
written 7 months ago by
annamariabugaj • 0
• updated
6 months ago by
Biostar ♦♦ 20
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... This is probably a stupid question but I really can not find an answer... I want to compare two DEGs sets from two different experimental settings in order to create a 'common DEGs set' and I found out that GSEA is a good way to do it but I need two types of files .gct and .cls
How do I create this ...
written 12 months ago by
annamariabugaj • 0
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... I have .bed files for TADs from experiments on neuronal fetal tissue downloaded from GEO (GSE77565). I need to extract the boundaries and I am not sure how long they should be. Is it ok to take 5kb flanks as you do for CCD boundaries?
...
written 2.5 years ago by
annamariabugaj • 0
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2.5 years ago by
igor ♦ 12k
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... I am conducting analyses based on 1000 Genomes paper and I am basically doing the same they did only using my own sets of data. But I am confused if it comes to p value - how do I estimate p value of enrichment(depletion) in such an analyses (the fragment from the 1000 genome paper below describes t ...
written 2.7 years ago by
annamariabugaj • 0
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... Hi,
I have a problem with data form DbVar - I need data from autism studies that is easy convertable to .bed since I want to intersect the CNVs with other genomic features. But the .txt file they offer is not tabular - is there any way to get this data in a nice tabular format? Another server maybe ...
written 3.5 years ago by
annamariabugaj • 0
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