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pGRN (version 0.3.5)

Single-Cell RNA Sequencing Pseudo-Time Based Gene Regulatory Network Inference

Description

Inference and visualize gene regulatory network based on single-cell RNA sequencing pseudo-time information.

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Version

Install

install.packages('pGRN')

Monthly Downloads

181

Version

0.3.5

License

MIT + file LICENSE

Maintainer

Gangcai Xie

Last Published

January 17th, 2023

Functions in pGRN (0.3.5)

slideWindows

Sliding Window Average
get_networks

Get the list of sub-networks
run_granger_test

Use Granger-causality Test to get gene-gene regulatory relationship
run_dtw

Get network adjacency dataframe based on DTW method
pGRN

pGRN: creates gene regulatory network based on single cell pseudotime information
pGRNDB

pGRN example data
plot_network_i

Plot interactive network
plot_network

Plot stationary network
matrix2adj

Convert distance matrix to adjacency dataframe
get_dtw_dist_mat

DTW distance matrix for all genes
module_networks

Get module level networks
data_transform

Pseudotime based Expression Data Transformation
get_dtw_dist_bidirectional

Bidirectional DTW Distance