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scapGNN
View on CRAN: Click
here
Download and install scapGNN package within the R console
Install from CRAN:
install.packages("scapGNN")
Install from Github:
library("remotes")
install_github("cran/scapGNN")
Install by package version:
library("remotes")
install_version("scapGNN", "0.1.4")
Attach the package and use:
library("scapGNN")
Maintained by
Xudong Han
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-06-10
Latest Update: 2023-08-08
Description:
It is a single cell active pathway analysis tool based on the graph neural network (F. Scarselli (2009) ; Thomas N. Kipf (2017) ) to construct the gene-cell association network, infer pathway activity scores from different single cell modalities data, integrate multiple modality data on the same cells into one pathway activity score matrix, identify cell phenotype activated gene modules and parse association networks of gene modules under multiple cell phenotype. In addition, abundant visualization programs are provided to display the results.
How to cite:
Xudong Han (2022). scapGNN: Graph Neural Network-Based Framework for Single Cell Active Pathways and Gene Modules Analysis. R package version 0.1.4, https://cran.r-project.org/web/packages/scapGNN
Previous versions and publish date:
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Other R packages that scapGNN depends,
imports, suggests or enhances
Functions, R codes and Examples using
the scapGNN R package
Some associated functions: ATAC_net . BIC_LTMG . BIC_ZIMG . ConNetGNN . ConNetGNN_data . Fit_LTMG . Global_Zcut . H9_0h_cpGM_data . H9_24h_cpGM_data . H9_36h_cpGM_data . Hv_exp . InteNet . LTMG-class . LTMG . Preprocessing . Pure_CDF . RNA_ATAC_IntNet . RNA_net . RWR . RunLTMG . cpGModule . create_scapGNN_env . instPyModule . isLoaded . load_path_data . plotCCNetwork . plotGANetwork . plotMulPhenGM . scPathway . scPathway_data .
Some associated R codes: ConNetGNN.R . InteNet.R . LTMG.R . Preprocessing.R . cpGModule.R . dataset.R . plotCCNetwork.R . plotGANetwork.R . plotMulPhenGM.R . scPathway.R . utils.R . Full scapGNN package functions and examples
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