This package is a suite of co-expression networks from the GTEx V6 gene expression data [https://gtexportal.org/home/]. It is useful with the CoExpNets package, here [https://github.com/juanbot/CoExpNets] which can be used to access and analyze these networks and to create new ones.
In the package you will find networks for the following tissues
> getGTExTissues()
[1] "AdiposeSub" "AdiposeVisceral" "AdrenalGland" "Amygdala" "AntCingCortex" "ArteryAorta"
[7] "ArteryCoronary" "ArteryTibial" "Breast" "Caudate" "CellsFirbroblasts" "CellsLymphocytes"
[13] "Cerebellum" "CerebHemisphere" "ColonSigmoid" "ColonTransverse" "Cortex" "EsophGastJunction"
[19] "EsophMucosa" "EsophMuscularis" "FCortex" "HeartAtrialApp" "HeartLeftVent" "Hippocampus"
[25] "Hypothalamus" "Liver" "Lung" "MuscleSkeletal" "NerveTibial" "NucAccumbens"
[31] "Ovary" "Pancreas" "Pituitary" "Prostate" "Putamen" "SkinLowerLeg"
[37] "SkinSuprapubic" "SmallIntestine" "Spinalcord" "Spleen" "Stomach" "Substantianigra"
[43] "Testis" "Thyroid" "Uterus" "Vagina" "WholeBlood" Each network is compound of
- An RDS file with the network itself. When reading the object you obtain a list with ´moduleColors´ and ´MEs´, the clustering of nodes and the module eigengenes respectively.
- A csv with the enrichment for the modules from the Gene Ontology, REACTOME and KEGG pathway annotation databases.
- The residuals (corrected by PMI, Age, Gender and Batch, with ComBat) and Surrogate variables with SVA.
Recommended that you install first CoExpNets
devtools::install_github('juanbot/CoExpNets')And then this package
devtools::install_github('juanbot/CoExpGTEx')