Package: mnda 1.0.9

mnda: Multiplex Network Differential Analysis (MNDA)

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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# Install 'mnda' in R:
install.packages('mnda', 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.

1.04 score 11 scripts 168 downloads 19 exports 91 dependencies

Last updated 2 years agofrom:2212095fc8. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winNOTENov 06 2024
R-4.5-linuxNOTENov 06 2024
R-4.4-winNOTENov 06 2024
R-4.4-macNOTENov 06 2024
R-4.3-winNOTENov 06 2024
R-4.3-macNOTENov 06 2024

Exports:as.igraphas.mnda.graphDistanceEDNNednn_IOprepareexample_datamnda_distance_test_isnmnda_embeddingmnda_embedding_2layermnda_node_detection_2layermnda_node_distancenetwork_genp_val_normp_val_rankRankRepRandomWalksubgraph_difference_plotsubgraph_plotWeightdRandomWalk

Dependencies:aggregationaskpassassertthatbackportsbase64enccachemclicliprcolorspaceconfigcpp11crayoncredentialscurldescdplyrfansifarverfastmapfsgenericsgertggforceggplot2ggraphggrepelghgitcredsgluegraphlayoutsgridExtragtableherehttr2igraphiniisobandjsonlitekeraslabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmeopensslpillarpkgconfigpngpolyclipprocessxpspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreticulaterlangrprojrootrstudioapiscalesstringistringrsyssystemfontstensorflowtfautographtfrunstibbletidygraphtidyrtidyselecttweenrusethisutf8vctrsviridisviridisLitewhiskerwithryamlzeallotzip