Package: PLEXI 1.0.0

PLEXI: Multiplex Network Analysis

Interactions between different biological entities are crucial for the function of biological systems. In such networks, nodes represent biological elements, such as genes, proteins and microbes, and their interactions can be defined by edges, which can be either binary or weighted. The dysregulation of these networks can be associated with different clinical conditions such as diseases and response to treatments. However, such variations often occur locally and do not concern the whole network. To capture local variations of such networks, we propose multiplex network differential analysis (MNDA). MNDA allows to quantify the variations in the local neighborhood of each node (e.g. gene) between the two given clinical states, and to test for statistical significance of such variation. Yousefi et al. (2023) <doi:10.1101/2023.01.22.525058>.

Authors:Behnam Yousefi [aut, cre, cph], Farzaneh Firoozbakht [aut]

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PLEXI.pdf |PLEXI.html
PLEXI/json (API)

# Install 'PLEXI' in R:
install.packages('PLEXI', repos = c('https://behnam-yousefi.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

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

1.00 score 119 downloads 21 exports 75 dependencies

Last updated 1 years agofrom:4bf3883e06. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winOKNov 01 2024
R-4.5-linuxOKNov 01 2024
R-4.4-winOKNov 01 2024
R-4.4-macOKNov 01 2024
R-4.3-winOKNov 01 2024
R-4.3-macOKNov 01 2024

Exports:as_igraphas_plexi_graphdistanceednnednn_io_prepareexample_datanetwork_genp_val_countp_val_normp_val_rankplexi_distance_test_isnplexi_distance_test1_isnplexi_embeddingplexi_embedding_2layerplexi_node_detection_2layerplexi_node_distanceRankrep_random_walksubgraph_difference_plotsubgraph_plotweightd_random_walk

Dependencies:aggregationassertthatbackportsbase64enccachemclicolorspaceconfigcpp11dplyrfansifarverfastmapgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtablehereigraphisobandjsonlitekeraslabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigpngpolyclipprocessxpspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreticulaterlangrprojrootrstudioapiscalesstringistringrsystemfontstensorflowtfautographtfrunstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewhiskerwithryamlzeallot