supportedCytokines

Returns the names of the cytokines supported by either the CytoSig or the Reactome databases.

Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021) <doi:10.1038/s41592-021-01274-5>. 'Reactome' database is described in: Gillespie et al., (2021) <doi:10.1093/nar/gkab1028>. The 'VAM' method is outlined in: Frost (2020) <doi:10.1093/nar/gkaa582>.

Azka Javaid

scaper

Single Cell Transcriptomics-Level Cytokine Activity Prediction
and Estimation

H. Robert Frost

supportedCytokines function

<dl><dt>database</dt>
<dd>Database used for gene set construction and set scoring.<ul>
<li>"cytosig" returns the 41 cytokines scored using the CytoSig database.</li>
<li>"reactome" returns the 30 cytokines scored using the Reactome database.</li>
</ul></dd></dl>

Arguments

Gene set to score for the CytoSig or the Reactome databases. — supportedCytokines

<dl>

<dt>database</dt>
<dd>Database used for gene set construction and set scoring.<ul>
<li>"cytosig" returns the 41 cytokines scored using the CytoSig database.</li>
<li>"reactome" returns the 30 cytokines scored using the Reactome database.</li>
</ul></dd>

</dl>

supportedCytokines: Gene set to score for the CytoSig or the Reactome databases.

Description

Usage

Value

Arguments

Examples