Graph Neural Network-Based Framework for Single Cell Active Pathways and Gene Modules Analysis

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Documentation for package ‘scapGNN’ version 0.1.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

.RunLTMG	Run Left-truncated mixed Gaussian
ATAC_net	Results of ConNetGNN() for scATAC-seq data from SNARE-seq dataset
BIC_LTMG	BIC_LTMG
BIC_ZIMG	BIC_ZIMG
ConNetGNN	Construct association networks for gene-gene, cell-cell, and gene-cell based on graph neural network (GNN)
ConNetGNN_data	The results of ConNetGNN() function
cpGModule	Identify cell phenotype activated gene module
create_scapGNN_env	Create the create_scapGNN_env environment on miniconda
Fit_LTMG	Fitting function for Left-truncated mixed Gaussian
Global_Zcut	Global_Zcut
H9_0h_cpGM_data	Cell-activated gene modules under the 0-hour phenotype
H9_24h_cpGM_data	Cell-activated gene modules under the 24-hour phenotype
H9_36h_cpGM_data	Cell-activated gene modules under the 36-hour phenotype
Hv_exp	Single-cell gene expression profiles
instPyModule	Install the pyhton module through the reticulate R package
InteNet	Integrate network data from single-cell RNA-seq and ATAC-seq
isLoaded	The internal functions of the 'scapGNN' package
load_path_data	load pathway or gene set's gmt file
LTMG	Left-truncated mixed Gaussian
LTMG-class	An S4 class to represent the input data for LTMG.
plotCCNetwork	Visualize cell cluster association network graph
plotGANetwork	Visualize gene association network graph of a gene module or pathway at the specified cell phenotype
plotMulPhenGM	Visualize gene association network graph for activated gene modules under multiple cell phenotypes
Preprocessing	Data preprocessing
Pure_CDF	Pure_CDF
RNA_ATAC_IntNet	Results of InteNet() for integrating scRNA-seq and scATAC-seq data.
RNA_net	Results of ConNetGNN() for scRNA-seq data from SNARE-seq dataset
RunLTMG	Run Left-truncated mixed Gaussian
RunLTMG-method	Run Left-truncated mixed Gaussian
RWR	Function that performs a random Walk with restart (RWR) on a given graph
scPathway	Infer pathway activation score matrix at single-cell resolution
scPathway_data	Single cell pathway activity matrix