R packages for applying Data mining or machine learning algorithms (SNV,RF, Neural Network) on RNAseq data

Question

[rahel14350]

Dear all, I have a set of differentially expressed genes. I want to use Data mining/machine learning R packages to see which set or pairs of genes are more related to each other on the function (to classify them and find potential biomarkers)? Basically to apply SNV, random forest and neural network algorithms on RNAseq data. Could you please recommend me any R packages to do so?

Many thanks in advance, Rahel

[Arup Ghosh]

Start with a pathway enrichment analysis.

[rahel14350]

Dear Arup,

Pathway analysis is not a part of Data mining/machine learning. I am looking for some packages to apply SNV or RF or Neural network algorithms on RNAseq data. Many thanks

Answer 1

[saanasum]

Maybe this helps to find a possible package: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633036/

[rahel14350]

Many thanks, this paper could be helpful! I am going to check it.