Gene Expression Analysis

In this workflow, we analyze RNA-Seq data from tumors and matched normal tissue from three patients with oral squamous cell carcinomas ( 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.

This is a companion discussion topic for the original entry at

I am trying to use this workflow either in a WebPortal, as you demonstrate, or 2) by downloading the workflow in Knime Analytics Platform.

  1. How can I use it in a WebPortal? I am not clear in which WebPortal I could find it.

  2. 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.

Hello @alishitz,

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.


Here ist an updated version:

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