Package: inferCSN 1.0.8

Meng Xu

inferCSN: Inferring Cell-Specific Gene Regulatory Network

An R package for inferring cell-type specific gene regulatory network from single-cell RNA data.

Authors:Meng Xu [aut, cre]

# Install 'inferCSN' in R:

install.packages('inferCSN', repos = c('https://mengxu98.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

Datasets:

On CRAN:

Last updated 10 days agofrom:b232096202. Checks:OK: 6 ERROR: 3. Indexed: yes.

Help page	Topics
_inferCSN_: inferring Cell-Specific gene regulatory Network	inferCSN-package
Convert dgCMatrix into a dense matrix	as_matrix
Calculate accuracy value	calculate_acc
Calculate AUPRC and AUROC values	calculate_auc
Rank TFs and genes in network	calculate_gene_rank
Check sparsity of matrix	check_sparsity
Extracts a specific solution in the regularization path	coef.srm coef.srm_cv
Example ground truth data	example_ground_truth
Example matrix data	example_matrix
Example meta data	example_meta_data
Filter and sort matrix	filter_sort_matrix
Fit a sparse regression model	fit_sparse_regression
inferring Cell-Specific gene regulatory Network	inferCSN inferCSN,data.frame-method inferCSN,matrix-method inferCSN,sparseMatrix-method
Print diagnostic message	log_message
Format network table	network_format
Sifting network	network_sift
Normalize numeric vector	normalization
Parallelize a function	parallelize_fun
Plot contrast networks	plot_contrast_networks
Plot dynamic networks	plot_dynamic_networks
Plot embedding	plot_embedding
Plot histogram	plot_histogram
Plot network heatmap	plot_network_heatmap
Plot expression data in a scatter plot	plot_scatter
Plot dynamic networks	plot_static_networks
Predicts response for a given sample	predict.srm predict.srm_cv
Prints a summary of 'fit_sparse_regression'	print.srm print.srm_cv
R^2 (coefficient of determination)	r_square
Construct network for single target gene	single_network
Sparse regression model	sparse_regression
Switch network table to matrix	table_to_matrix