CellRouter: The CellRouter class.
In edroaldo/fusca: Framework for Unified Single-Cell Analysis

CellRouter-class

R Documentation

The CellRouter class.

Description

An S4 class to represent the CellRouter object and its contents.

Details

A multifaceted single-cell analysis platform that identifies complex cell-state transition trajectories by using flow networks to explore the subpopulation structure of multi-dimensional, single-cell omics data.

Slots

assays: list; different data used in the analysis.
sampTab: data frame; store the information of the integrated analysis of multiple assays.
rdimension: data frame; cell embeddings from PCA.
pca: list; data from principal component analysis.
tsne: list; data from t-SNE dimensionality reduction.
umap: list; data from UMAP dimensionality reduction.
dr.custom: list; data from custom dimensionality reduction.
dc: list; data from dc dimensionality reduction.
custom: list; cell embeddings for custom space.
var.genes: A character.
graph: A list.
signatures: A list.
sources: A character.
targets: A character.
directory: list; directories of files obtained in the findPaths method.
paths: data frame; paths between populations.
networks: list; graphs between populations.
genes.trajectory: character vector; genes considered in the trajectories.
pathsinfo: list; information about the paths across populations.
dynamics: list; the smoothed correlations between gene expression and pseudotime in paths between populations.
clusters: list; the clusters for the selected trajectories.
correlation: list; correlations between gene expression and pseudotime in paths between populations.
top.correlations: list; gene trends (up or down) for each path.
pathwayenrichment: list; pathway enrichment analysis on genes up or down-regulated along trajectories.
curves: list; the curves for the specified paths.