In this workflow, we analyze RNA-Seq data from tumors and matched normal tissue from three patients with oral squamous cell carcinomas (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009317). Differentially expressed genes are discovered using the R package edgeR and are then displayed in an interactive view. Subsequently, genes are hierarchically clustered based on their expression pattern, and the results are shown via a dendrogram alongside a heatmap. We then perform a pathway enrichment analysis and look for compounds targeting the gene product of interest.
I am trying to use this workflow either in a WebPortal, as you demonstrate, or 2) by downloading the workflow in Knime Analytics Platform.
How can I use it in a WebPortal? I am not clear in which WebPortal I could find it.
After I downloaded the workflow in Knime Analytics Platform installed on my Windows 10 machine (not Linux), I tried to execute it. The 3rd node in the workflow, R Snippet, gives below error message, which indicates EdgeR is not installed correctly:
ERROR R Snippet 3:566 Execute failed: Error in R code: *
Installing package into ‘C:/Users/Ariel.Lifshitz/Documents/R/win-library/4.1’*
(as ‘lib’ is unspecified)*
Error: there is no package called ‘edgeR’*
I assume this problem is related to extension KNIME4NGS not being available to me. I followed the installation steps as described on the help page Knime4NGS however I believe it was not installed correctly. The instructions mention as a prerequisite Linux. I was informed that “Some nodes may also work in a KNIME installation on Windows. However, as our developed nodes are mostly wrapping other Linux dependent tools such as BWA, GATK, etc., you should install KNIME4NGS in a KNIME installation on a Linux machine.”
Thus, I wonder whether I’m wrong in my attempt to use this demo workflow on a Windows machine, or perhaps I’m doing something wrong trying to install extension KNIME4NGS and the edgeR package.
Regarding your first question about the WebPortal, the WebPortal is available in our Commercial offering. The KNIME Serverr (software) has this capability in addition to automation, collaboration, security, and monitoring.
I am not sure about the answer for your second question but you could try installing the R package. Here are some tips. I am not familiar with the KNIME4NGS extension.