Loading the example data | Call pGRN | plot the network
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:
pGRN_0.3.5.tar.gz
pGRN_0.3.5.zip(r-4.7-any)pGRN_0.3.5.zip(r-4.6-any)pGRN_0.3.5.zip(r-4.5-any)
pGRN_0.3.5.tgz(r-4.6-any)pGRN_0.3.5.tgz(r-4.5-any)
pGRN_0.3.5.tar.gz(r-4.7-any)pGRN_0.3.5.tar.gz(r-4.6-any)
pGRN_0.3.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:f82aaedb03. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 264 | ||
| source / vignettes | OK | 217 | ||
| linux-release | OK | 188 | ||
| macos-release | OK | 239 | ||
| macos-oldrel | OK | 199 | ||
| windows-devel | OK | 163 | ||
| windows-release | OK | 138 | ||
| windows-oldrel | OK | 139 | ||
| wasm-release | OK | 151 |
Exports:data_transformget_dtw_dist_bidirectionalget_dtw_dist_matget_networksmatrix2adjmodule_networkspGRNplot_networkplot_network_irun_dtwrun_granger_testslideWindows
Dependencies:base64encBHbigmemorybigmemory.sribslibcachemclicodetoolscpp11digestdoParalleldplyrdtwevaluatefarverfastmapfontawesomeforeachfsfuturegenericsggforceggplot2ggraphggrepelglobalsgluegraphlayoutsgridExtragtablehighrhtmltoolshtmlwidgetsigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelistenvlmtestmagrittrMASSMatrixmemoisemimeparallellypillarpkgconfigpolyclipproxypurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownS7sassscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttinytextweenrutf8uuidvctrsviridisviridisLitevisNetworkwithrxfunyamlzoo
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 |