We have a list of differentially expressed genes from a RNA-seq experiment, including the fold changes p-values etc.
Our goal is to link these genes to drugs that have influences on these genes. This could lead to potential drugs that can help to induce or delay a diseased phenotype(maybe delete).
From our research we have found several interesting packages from bioconductor that may help to contribute to our goal, which are : gCMAP,gCMAPWeb and DrugVsDisease(DVD).
We do not have any experience with these packages and are unsure if we can use them. From the documentation the DrugVSDisease package may suite the best, and has a good manual. But this is meant for microarray data. The gCMAP(Web) mentions RNA-seq data in their manual but does seem to lack the ability to link to diseases.
Is it possible ( and reliable/easy ) to use a combination of the packages, so use the DVD package with RNA-seq result data?
What is the best approach for our research in finding drugs of interest and have some background information about which diseases are associated with these ?
We want to use R for our experiment, so for example the cmap web tool would not be the right choice.
We are very grateful for any help in regards to this matter !