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License: Creative Commons Zero v1.0 Universal
collection of notebooks with different cytoscape workflows
License: Creative Commons Zero v1.0 Universal
query_microarray <- GDCquery(project = "TCGA-OV",
data.category = "Raw microarray data",
data.type = "Normalized intensities",
platform = "HT_HG-U133A",
access = "open",
legacy = TRUE)
GDCdownload(query_microarray )
HI guys
It is not an issue it a question regarding enrichmenet analysis.
Do you recommend running pathway analysis without FDR cutt-off so it is independent of DGE genes?
I am a bit new to rnaseq so your comments are helpful.
M
Cotyoscape has helped me a lot ,but now I meet a problem when i use the function 'mapdata' .
I want to do a function like color gradual change , to use 3 values and 3colors like {'background-color': 'mapData(width,1,10,50,color1,color2,color3)'} , but the document says it supports only 2 values, i want to know a way to deal with it,can you help me ? thanks a lot.
Hi,
The cytoscape plugin hints that we could use the outputs from EnrichR( https://maayanlab.cloud/Enrichr/ ) . I was wondering if there is a tutorial on how get the gmt files from EnrichR and how to use the outputs for enrichment Map ?
Thanks
Yaseswini
Hi Bader,
My research species is a non-model organism, Anopheles stephensi. I wonder can we use this workflow?
Thanks
query <- GDCquery(project = "TCGA-OV",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts",
legacy = FALSE)
)
Hello,
I have been working on R generating my GSEA output by using the gseGO function from the clusterprofiler R package. However, I had a lot of issues trying to modify or set my data to be plotted on enrichment map by using the emcommand from the RCy3 package. I was wondering if you could provide insight into what I can do to visualize my GSEA data to the enrichment map?
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