# Gene Expression Analysis **URL:** \ **Category:** KCH Workflows\ **Created:** [September 8, 2020, 6:28am UTC](https://forum.knime.com/t/gene-expression-analysis/26936 "2020-09-08T06:28:52Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Hub](https://forum-cdn.knime.com/user_avatar/forum.knime.com/hub/32/5438_2.png) [@Hub](https://forum.knime.com/u/Hub)\ **Post date:** [September 8, 2020, 6:28am UTC](https://forum.knime.com/t/gene-expression-analysis/26936/1 "2020-09-08T06:28:53Z")
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. * * * This is a companion discussion topic for the original entry at [https://kni.me/w/rqle\_MONRctf7nGs](https://kni.me/w/rqle_MONRctf7nGs) ---
**Author:** ![alifshitz](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/a/e8c25b/32.png) [@alifshitz](https://forum.knime.com/u/alifshitz)\ **Post date:** [February 4, 2022, 5:58am UTC](https://forum.knime.com/t/gene-expression-analysis/26936/2 "2022-02-04T05:58:50Z")
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](http://ibisngs.github.io/knime4ngs/#:~:text=Download%20and%20Install%20Nodes&text=and%20add%20http%3A%2F%2Fibisngs,and%20install%20the%20displayed%20package) 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. ---
**Author:** ![cpadilla](https://forum-cdn.knime.com/user_avatar/forum.knime.com/cpadilla/32/18329_2.png) [@cpadilla](https://forum.knime.com/u/cpadilla)\ **Post date:** [April 27, 2022, 8:57pm UTC](https://forum.knime.com/t/gene-expression-analysis/26936/3 "2022-04-27T20:57:38Z")
Hello @alishitz, Regarding your first question about the WebPortal, the WebPortal is available in our Commercial offering. The [KNIME Server](https://www.knime.com/knime-server)r (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](https://forum.knime.com/t/install-r-alongside-knime-on-windows-and-macos/13287) are some tips. I am not familiar with the KNIME4NGS extension. Regards, Cynthia ---
**Author:** ![mlauber71](https://forum-cdn.knime.com/user_avatar/forum.knime.com/mlauber71/32/73590_2.png) [@mlauber71](https://forum.knime.com/u/mlauber71)\ **Post date:** [April 27, 2022, 9:22pm UTC](https://forum.knime.com/t/gene-expression-analysis/26936/4 "2022-04-27T21:22:49Z")
> [@cpadilla](#): > > installing the R package Here ist an updated version: > **[A meta collection and article about R and KNIME – mlauber71](https://hub.knime.com/mlauber71/spaces/Public/_r_installation_on_knime_collection~tj5tS_6gYvqOSPlk/current-state)** > > A meta collection and article about R and KNIME R gives you the power to do a lot of great things combined with KNIME but to get R and KNIME together up and ru… [https://docs.knime.com/latest/r\_installation\_guide/index.html#\_introduction](https://docs.knime.com/latest/r_installation_guide/index.html#_introduction)