Knime for Gene Expression Analysis

KNIME Analytics Platform
1

Hello
Is there any extension or nodes that can deal with data of gene expression (Bioinformatics) that can, for example, remove noisy genes (filter out rows of noise data ). I’m looking for something that is similar to the Bioinformatics package of Matlab
https://www.mathworks.com/help/bioinfo/examples/gene-expression-profile-analysis.html#d120e5897

Best
Malik

2

Hi,

Have you checked the categories at https://nodepit.com/category/?
You may find what you need there.

Best,
Armin

1 Like
3

Hi Malik,

there is no one-node solution like this, but there are many nodes that are useful in this context depending on your specific goal.

Here are some examples of nodes you could use to do tasks like provided in the documentation of the package:

  • Row Filter node for filtering rows according to certain criteria (including missing values)
  • Low Variance Filter node for filtering genes with small/high variance
  • Hierarchical clustering, k-means clustering nodes
  • PCA
  • Different nodes for visualization: Heatmaps, Dendrograms (from the node Hierarchical Cluster Assigner (JavaScript))
  • Normalizer node for data normalization

Additionally you could also use scripting nodes with your favourite library/package for those functionalities where nodes aren’t available.

Best,
Martyna

1 Like
4