Gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray or RNAseq samples.
Most of the tools i've found still use pearson correlation to detect co-expression between samples ( like the WGCNA package ). Is there a commonly used tool i've missed maybe?
Try the follwoing free online version which is great tool to do network analysis!
http://metascape.org/gp/index.html#/main/step1
Try the follwoing free online version which is great tool to do network analysis!
http://metascape.org/gp/index.html#/main/step1
WGNCA is a reliable package, hence people are using it for microarray as well as for RNA-seq data. Simply we can say, if you are having differential expression data, WGCNA is best package.
We have integrated PCC, SCC, GO score and FPKM values for our analysis and it has given fruitful insight about our data. You may refer given article.
https://www.nature.com/articles/s41598-017-14973-x
ARACNE is not properly based on the classical co-expression methods, but might be useful. It is designed for microarray data.
Article ARACNE: An Algorithm for the Reconstruction of Gene Regulato...
Try STRING (https://string-db.org/). It is not for co-expression per se but once you feed in the gene list you could do variety of things. Just play. It also uses information from other species
Try CoRegNet: reconstruction and integrated analysis of co-regulatory networks
https://bioconductor.org/packages/release/bioc/html/CoRegNet.html
Self-promotion like answer - :)
Best regards, Mohamed.
https://cytoscape.org/download.html
http://www.omicsnet.ca.
https://www.biostars.org/t/network/
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