All Questions
9 questions
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How can I associate centrality score of genes(vertices) in a GRN with the probabilistic model in terms of cause and effect?
I'm learning to build Bayesian Network Based Modeling of Gene Regulatory Network of Cancerous Cellular Cells. So far, I have learned to form a Bayesian Network based on nature of genes(i.e Functional ...
- 111
1
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1
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713
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Clustering of gene co-expression network by igraph R package
I have constructed a gene co-expression network from RNA-seq data. The network has more than 10000 nodes and more than 1 million edges.
The network file as an edge list format of memory around 1gb ...
0
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1
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306
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How do I get the adjacency matrix from gene similarity network?
I am exploring application of Graph convolution network on gene similarity network. I am trying to explore
genemania.org and https://string-db.org/
Please let me know where can I find the data for my ...
Susha Suresh
0
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1
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72
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How to create a graph of multi column gene dataset?
well, I'm new to Bio. what I'm going to do is create a network/graph of a dataset related to the genes I think. here's the sample of the nodes dataset with CSV format named lung-nodes :
and this is ...
- 129
7
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2
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201
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Are gene names same across species?
I have a bunch of gene names of Apis mellifera (specifically 194). I used these gene names as an input on STRING database to create a network for Drosophila melanogaster. 54 of those genes were also ...
- 297
3
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1
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63
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How to read gene regulatory network edge list files?
The following is an excerpt from an edge list file from the Gene Regulatory Database, YeastNet v3
...
- 139
2
votes
0
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95
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Locate KEGG/Reactome pathways in user defined network
I am working on big networks of genes. I want to locate KEGG/Reactome pathways in my network. I have already tried cytoKegg and ReactomeFI (Plugins of Cytoscape), they only give me a list of Pathways ...
- 121
1
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0
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82
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Help with generating network from gene expression data
I'm struggling to figure out how to go from gene expression data to be able to create a network out of the most expressed genes in a cell line. Ok, I have developed an application for Cytoscape where ...
- 109
10
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4
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890
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How can I build a protein network pathway from a gene expression quantification file?
Assume I have found the top 0.01% most frequent genes from a gene expression file.
Let's say, these are 10 genes and I want to study the protein protein interactions, the protein network and pathway....
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