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netZoo / netZooR

netZooR is a network biology package implemented in R.
https://netzoo.github.io/
GNU General Public License v3.0
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What's the pipeline for this tool #186

Closed echoduan closed 3 years ago

echoduan commented 3 years ago

Hello,

 I want to detect the network and target genes relying on the RNA-seq data. I think your tool (netZooR) may be helpful. I have installed it and Cytoscape on my linux platform successfully. But I don't how to utilize your tool relying on the Different expression genes list.

Could you share the pipeline with me please?

marouenbg commented 3 years ago

Hi @echoduan ,

netZooR is package of tools that allow to build networks and analyze them. The tools that allow to reconstruct a network from gene expression are MONSTER, OTTER, PANDA, PUMA. Check the vignettes in R for the usage as well as jupyter notebooks.

echoduan commented 3 years ago

Hi, Thanks for your reply.

 Whether did the files:(ppi_GTEx.txt and motif_GTEx.txt) include all potential genes in human? Can I directly utilize the interaction list in other research in human?
marouenbg commented 3 years ago

Yes you can use them in other research, however they don't include all genes. You can increase the coverage bu scanning the genome against TF motif sequence. You can use CIS-BP as database for TF motif, the latest human genome sequence hg38, and a scanning tool such as FIMO. More details can be found here

marouenbg commented 3 years ago

Hi @echoduan , closing this for now, please feel free to use discussions if you have any question!