Package: pGRN 0.3.5

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

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

Authors:Gangcai Xie

pGRN_0.3.5.tar.gz
pGRN_0.3.5.zip(r-4.5)pGRN_0.3.5.zip(r-4.4)pGRN_0.3.5.zip(r-4.3)
pGRN_0.3.5.tgz(r-4.4-any)pGRN_0.3.5.tgz(r-4.3-any)
pGRN_0.3.5.tar.gz(r-4.5-noble)pGRN_0.3.5.tar.gz(r-4.4-noble)
pGRN_0.3.5.tgz(r-4.4-emscripten)pGRN_0.3.5.tgz(r-4.3-emscripten)
pGRN.pdf |pGRN.html✨
pGRN/json (API)

# Install 'pGRN' in R:

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

Datasets:

pGRNDB - PGRN example data

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 3 scripts 182 downloads 12 exports 89 dependencies

Last updated 2 years agofrom:f82aaedb03. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 20 2024
R-4.5-win	OK	Nov 20 2024
R-4.5-linux	OK	Nov 20 2024
R-4.4-win	OK	Nov 20 2024
R-4.4-mac	OK	Nov 20 2024
R-4.3-win	OK	Nov 20 2024
R-4.3-mac	OK	Nov 20 2024

Exports:data_transform get_dtw_dist_bidirectional get_dtw_dist_mat get_networks matrix2adj module_networks pGRN plot_network plot_network_i run_dtw run_granger_test slideWindows

Dependencies:base64enc BH bigmemory bigmemory.sri bslib cachem cli codetools colorspace cpp11 digest doParallel dplyr dtw evaluate fansi farver fastmap fontawesome foreach fs future generics ggforce ggplot2 ggraph ggrepel globals glue graphlayouts gridExtra gtable highr htmltools htmlwidgets igraph isoband iterators jquerylib jsonlite knitr labeling lattice lifecycle listenv lmtest magrittr MASS Matrix memoise mgcv mime munsell nlme parallelly pillar pkgconfig polyclip proxy purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen rlang rmarkdown sass scales stringi stringr systemfonts tibble tidygraph tidyr tidyselect tinytex tweenr utf8 uuid vctrs viridis viridisLite visNetwork withr xfun yaml zoo

pGRN: scRNA-Seq Pseudotime Based Gene Regulatory Netowrk Inference

Gangcai Xie

Rendered frompGRN.Rmdusingknitr::knitron Nov 20 2024.

Last update: 2023-01-17
Started: 2023-01-17

Citation

Readme and manuals

Help Manual

Help page	Topics
Pseudotime based Expression Data Transformation	data_transform
Bidirectional DTW Distance	get_dtw_dist_bidirectional
DTW distance matrix for all genes	get_dtw_dist_mat
Get the list of sub-networks	get_networks
Convert distance matrix to adjacency dataframe	matrix2adj
Get module level networks	module_networks
pGRN: creates gene regulatory network based on single cell pseudotime information	pGRN
pGRN example data	pGRNDB
Plot stationary network	plot_network
Plot interactive network	plot_network_i
Get network adjacency dataframe based on DTW method	run_dtw
Use Granger-causality Test to get gene-gene regulatory relationship	run_granger_test
Sliding Window Average	slideWindows

Usage by other packages (reverse dependencies)