baderlab / cytoscape_workflows Goto Github PK

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

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?

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

query <- GDCquery(project = "TCGA-OV",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts",
legacy = FALSE)
)

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 )

RMA normalized are recommended over MAS5.0 level3 data