LRI_mouse

This dataset contains a data.table of curated mouse ligand-receptor
 interactions as well as related annotations (GO Terms, KEGG Pathways) and
 metadata.

datasets

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

LRI_mouse function

A list with the following items:<ol>
<li><code>LRI_curated</code>: a data.table of curated LRIs</li>
<li><code>LRI_curated_GO</code>: a data.table with GO terms attached to
 curated LRI</li>
<li><code>LRI_curated_KEGG</code>: a data.table with KEGG pathways attached to
 curated LRIs</li>
<li><code>LRI_retrieved_dates</code>: dates at which data have been retrieved
 from the seven external databases</li>
<li><code>LRI_retrieved_from</code>: paths or packages from where data have
 been retrieved</li>
<li><code>LRI_biomart_ensembl_version</code>: version of ensembl used for
 GO annotation and orthology conversion</li>
</ol>

LRI_mouse: A collection of mouse ligand-receptor interactions.

Description

Usage

Arguments

Format

Details

References