ReduceGO

ReduceGO,scDiffCom-method

Perform semantic similarity analysis and reduction of the
 overrepresented GO terms of an scDiffCom object.

Analysis tools to investigate changes in intercellular
communication from scRNA-seq data. Using a Seurat object as input,
the package infers which cell-cell interactions are present in the dataset
and how these interactions change between two conditions of interest
(e.g. young vs old). It relies on an internal database of ligand-receptor
interactions (available for human, mouse and rat) that have been gathered
from several published studies. Detection and differential analyses
rely on permutation tests. The package also contains several tools
to perform over-representation analysis and visualize the results. See
Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full
description of the methodology.

Cyril Lagger

scDiffCom

Differential Analysis of Intercellular Communication from
scRNA-Seq Data

Eugen Ursu

Anais Equey

ReduceGO function

<dl><dt>object</dt>
<dd><code>scDiffCom</code> object</dd>
<dt>method</dt>
<dd>A distance method supported by rrvgo and GOSemSim:
c("Rel", "Resnik", "Lin", "Jiang", "Wang")</dd>
<dt>threshold</dt>
<dd>Similarity threshold used by <code>rrvgo::reduceSimMatrix</code></dd></dl>

Arguments

Reduce scDiffCom GO Terms — ReduceGO

<dl>

<dt>object</dt>
<dd><code>scDiffCom</code> object</dd>


<dt>method</dt>
<dd>A distance method supported by rrvgo and GOSemSim:
c("Rel", "Resnik", "Lin", "Jiang", "Wang")</dd>


<dt>threshold</dt>
<dd>Similarity threshold used by <code>rrvgo::reduceSimMatrix</code></dd>

</dl>

ReduceGO: Reduce scDiffCom GO Terms

Description

Usage

Value

Arguments

Details