User: mrashad

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mrashad50
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Posts by mrashad

<prev • 44 results • page 1 of 5 • next >
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p-adjusted threshold in pathfindR
... Dears, I make a differential expression analysis using t test by multtest package in R under conditions of p-value < 0.05. So the output of this step is group of genes with significant p values and partially significant p adjusted values as shown in this link: https://ibb.co/LDF9CBV I used this ...
#pathway_enrichment_analysis written 5 days ago by mrashad50
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Comment: A: Enrichment Analysis, Clustering and Scoring with pathfindR
... Dear, thanks a lot for this tutorial. But, If I want to get the p adjusted for the pathways in the output result as you know the output contain lowest p value and highest p value not the p adjusted. How I can do that ? I tried to use p.adjust function in R, is it right way or not ? if not, is there ...
written 8 days ago by mrashad50
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Visualization of common pathways
... Dears, I need to visualize the pathways that common between RNA data and cytokine data with explaining the contribution of each gene and cytokine. Note that the digits in the columns of RNA and cytokine is p value. https://ibb.co/17PSTkP Thanks, ...
#visualization #common_pathways written 21 days ago by mrashad50
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Tissue specificity for metabolites and bacteria
... Dear, I have sample of metabolites and bacteria sampled from group of patients through blood and gut/nasal cavity respectively. Is there a tool helping me to determine if these metabolites are specific for blood or not ( tissue specified ) and the same for the bacteria to gut /nasal cavity ? I need ...
#metabolome #metagenome written 4 weeks ago by mrashad50
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Comment: C: Heatmaps by pheatmap
... That's it, It works with Complexheatmap. Thanks a lot for this fruitful answer ...
written 5 weeks ago by mrashad50
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Heatmaps by pheatmap
... Dear I make the following heatmap using pheatmap package, but I need to put a title for legend. How to make that ? if there is other package better than pheatmap make a clustering for rows and columns + can make a title for legend through it, please tell me about it. https://ibb.co/VQM7px0 ...
#visualization written 5 weeks ago by mrashad50 • updated 5 weeks ago by k.nirmalraman1.1k
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Comment: A: scale free topology in WGCNA
... Honestly, it is the first time for me to use WGCNA and I used this tutorial as a guide: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-auto.pdf + video for its author: https://www.youtube.com/watch?v=rRIRMW_RRS4 but there is no step ...
written 6 weeks ago by mrashad50
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scale free topology in WGCNA
... Dear this image resulted from plotting the result of picksoftthreshold function in WGCNA ![scale_free and mean connectivity][1] I need to ask what is the meaning of the sft result from using picksoftthreshold function in WGCNA as this result is considered as a list contain powerestimate which equal ...
#network_analysis #wgcna written 6 weeks ago by mrashad50
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Comment: C: Diseases related pathways
... I got it now, thanks a lot. The first link is used if you search for any pathway that contain "diabetes" anywhere, while the other link mentions all pathways in Diabetes disease through KEGG disease database. ...
written 6 weeks ago by mrashad50
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Comment: C: Diseases related pathways
... Thanks a lot for this fruitful answer ...
written 6 weeks ago by mrashad50

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