Package: NetRep 1.2.4

NetRep: Permutation Testing Network Module Preservation Across Datasets

Functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing; Ritchie et al. (2015) <doi:10.1016/j.cels.2016.06.012>.

Authors:Scott Ritchie [aut, cre]

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NetRep.pdf |NetRep.html✨
NetRep/json (API)

# Install 'NetRep' in R:

install.packages('NetRep', repos = c('https://sritchie73.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sritchie73/netrep/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

discovery_correlation - Example data
discovery_data - Example data
discovery_network - Example data
module_labels - Example data
test_correlation - Example data
test_data - Example data
test_network - Example data

On CRAN:

openblas cpp

6.84 score 12 stars 3 packages 16 scripts 464 downloads 8 mentions 21 exports 10 dependencies

Last updated 4 years agofrom:1a62bad2ea. Checks:1 OK, 5 NOTE, 6 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 07 2025
R-4.5-win-x86_64	NOTE	Mar 07 2025
R-4.5-mac-x86_64	WARNING	Mar 07 2025
R-4.5-mac-aarch64	WARNING	Mar 07 2025
R-4.5-linux-x86_64	NOTE	Mar 07 2025
R-4.4-win-x86_64	NOTE	Mar 07 2025
R-4.4-mac-x86_64	WARNING	Mar 07 2025
R-4.4-mac-aarch64	WARNING	Mar 07 2025
R-4.4-linux-x86_64	NOTE	Mar 07 2025
R-4.3-win-x86_64	NOTE	Mar 07 2025
R-4.3-mac-x86_64	WARNING	Mar 07 2025
R-4.3-mac-aarch64	WARNING	Mar 07 2025

Exports:as.disk.matrix as.matrix attach.disk.matrix combineAnalyses is.disk.matrix load.bigMatrix modulePreservation networkProperties nodeOrder permutationTest plotContribution plotCorrelation plotData plotDegree plotModule plotNetwork plotSummary requiredPerms sampleOrder serialize.table show

Dependencies:abind BH codetools foreach iterators RColorBrewer Rcpp RcppArmadillo RhpcBLASctl statmod

NetRep

Scott Ritchie

Rendered fromNetRep.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2018-06-12
Started: 2016-02-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The 'disk.matrix' class	as.disk.matrix as.disk.matrix,ANY-method as.disk.matrix,disk.matrix-method as.disk.matrix,matrix-method as.matrix,disk.matrix-method attach.disk.matrix disk.matrix is.disk.matrix serialize.table show,disk.matrix-method
Example data	discovery_correlation discovery_data discovery_network example-data module_labels NetRep-data test_correlation test_data test_network
Replication and preservation of network modules across datasets	modulePreservation
Fast permutation procedure for testing network module replication	NetRep
Calculate the topological properties for a network module	networkProperties
Plot the topology of a network module	plotModule
How many permutations do I need to test at my desired significance level?	requiredPerms