Any Cast

Removes type information for the fronted, so you can artificially combine nodes that have conflicting type information. This is only useful to allow certain edge cases where the types are not correctly inferred.

Example use case: A node generally returns a union and does not dynamically update its output type, but you know for sure that a specific variant will be returned. As long as the node specifies the union as its output type, you cannot pass it into another node requiring that specific variant. In this case, the Any Cast node comes in handy.

Input: The previous node output you want to remove the type information from.

Output: The input with removed type information.

Batch

Enables batch processing of values. Provides an array of input values and gets every element from that array one-by-one to process them separately.

Input: An array of any type. These are the values the batch node will be iterating over.

Output: For each element of the input: the element and its index in the list.

GO Enrichment

Computes a Ontology (GO) enrichment based upon a provided gene set.

The GO database classifies gene functions into three main categories: Biological Processes, Molecular Functions, Cellular Components. In an enrichment analysis, a set of genes of interest, e.g., differentially expressed genes, is compared against a background set of all genes, to determine which GO terms are statistically overrepresented in the dataset. At the moment, the background set always contains all genes of a certain organism. Soon, an option to manually set the background set will be provided.

Input: Gene Set as csv file.

Requirements: Each row refers to a gene name. In addition to the gene names, the following columns must exist:

• p value: unadjusted
• avg_log2FC: Logarithmic fold change of average expression. Positive values mean that the gene is higher expressed in the first group.
• pct. 1: Percentage of cells in which the gene is detected in for the first group.
• pct. 2: Percentage of cells in which the gene is detected in for the second group.
• p_val_adj: p value adjusted by Bonferroni correction.

Input Parameters:

• Ontology Type: Desired ontology type (BP, MF, CC, all)
• Gene name format: Format of the gene names provided in the input dataset (SYMBOL, ENTREZID)

Output: Enriched gene set as csv file. Can be plotted in a bar plot. More plots will be provided soon.

Citations:

Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000 May;25(1):25-9. DOI: 10.1038/75556

The Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031. DOI: 10.1093/genetics/iyad031

Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou LP, Mi H. PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci. 2022 Jan;31(1):8-22. DOI: 10.1002/pro.4218

GO Term Barplot

Plots a bar plot of the GO enrichment result (enriched gene set).

Input: Enriched gene/term set from GO Enrichment node.

Output: Generated plot. Can be viewed with Image Viewer (see Visualization).

Range

Creates a range of integer numbers as an array.

Input:

• Start: Lower bound of the range (included).
• Stop: Upper bound of the range (excluded).

Output: An array containing the numbers [Start, Stop].