annotation_data_sources

A data.frame/tibble describing for each type of data source the "parent" database and type of interactions it countains.

datasets

This package allows you the investigate intercellular communication from a computational perspective. More specifically, it allows to investigate how interacting cells influence each other's gene expression. Functionalities of this package (e.g. including predicting extracellular upstream regulators and their affected target genes) build upon a probabilistic model of ligand-target links that was inferred by data-integration.

Robin Browaeys

nichenetr

NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

annotation_data_sources function

A data frame/tibble<dl class="dl-horizontal">
 <dt>source</dt><dd>Name of the data source</dd>
 <dt>database</dt><dd>Name of the comprehensive database to which the data source belongs</dd>
 <dt>type_db</dt><dd>Type of data source</dd>
 <dt>type_interaction</dt><dd>Interaction type</dd>
 <dt>network</dt><dd>Network layer to which the data source belongs: ligand_receptor, signaling or gene_regulatory</dd>
 </dl>

Format

Annotation table of all data sources used in the NicheNet model — annotation_data_sources

A data frame/tibble<dl class='dl-horizontal'>
 <dt>source</dt><dd>Name of the data source</dd>
 <dt>database</dt><dd>Name of the comprehensive database to which the data source belongs</dd>
 <dt>type_db</dt><dd>Type of data source</dd>
 <dt>type_interaction</dt><dd>Interaction type</dd>
 <dt>network</dt><dd>Network layer to which the data source belongs: ligand_receptor, signaling or gene_regulatory</dd>
 </dl>

annotation_data_sources: Annotation table of all data sources used in the NicheNet model

Description

Usage

Arguments

Format