Package: BioNAR 1.15.0

Anatoly Sorokin

BioNAR: Biological Network Analysis in R

the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.

Authors:Colin Mclean [aut], Anatoly Sorokin [aut, cre], Oksana Sorokina [aut], J. Douglas Armstrong [aut, fnd], T. Ian Simpson [ctb, fnd]

BioNAR_1.15.0.tar.gz
BioNAR_1.15.0.zip(r-4.7)BioNAR_1.15.0.zip(r-4.6)BioNAR_1.15.0.zip(r-4.5)
BioNAR_1.15.0.tgz(r-4.6-any)BioNAR_1.15.0.tgz(r-4.5-any)
BioNAR_1.15.0.tar.gz(r-4.7-any)BioNAR_1.15.0.tar.gz(r-4.6-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BioNAR/json (API)

# Install 'BioNAR' in R:

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

Bug tracker:https://github.com/lptolik/bionar/issues

Datasets:

diseasome - Barabasi's Diseasome Network

On BioConductor:BioNAR-1.15.0(bioc 3.24)BioNAR-1.14.0(bioc 3.23)

software graphandnetwork network

5.22 score 3 stars 37 scripts 366 downloads 72 exports 123 dependencies

Last updated from:5acd4d1e61. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	269
linux-devel-x86_64	NOTE	550
source / vignettes	OK	460
linux-release-x86_64	NOTE	512
macos-release-arm64	NOTE	300
macos-oldrel-arm64	NOTE	269
windows-devel	NOTE	466
windows-release	NOTE	523
windows-oldrel	NOTE	488
wasm-release	OK	234

Exports:addEdgeAtts annotateGeneNames annotateGoBP annotateGoCC annotateGoMF annotateGOont annotateInterpro annotatePresynaptic annotateSCHanno annotateTopOntoOVG annotateVertex applpMatrixToGraph buildConsensusMatrix buildNetwork calcAllClustering calcBridgeness calcCentrality calcCentralityExternalDistances calcCentralityInternalDistances calcClustering calcDiseasePairs calcEntropy calcMembership calcReclusterMatrix calcSparsness clusteringSummary clusterORA degreeBinnedGDAs escapeAnnotation evalCentralitySignificance findLCC fitDegree fitSigmoid getAnnotationList getAnnotationVertexList getBridgeness getCentralityMatrix getClustering getClusterSubgraphByID getCommunityGraph getDiseases getDType getDYNAMO getEntropy getEntropyRate getGNP getGraphCentralityECDF getPA getRandomGraphCentrality getRobustness gofs layoutByCluster layoutByRecluster makeConsensusMatrix makeMembership markBowTie metlMatrix normModularity permute plotBridgeness plotEntropy plotRatio plotSigmoid prepareGDA recluster removeVertexTerm runPermDisease sampleDegBinnedGDA sampleGraphClust summaryStats unescapeAnnotation zeroNA

Dependencies:AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob bslib cachem checkmate cli cluster codetools colorspace cowplot cpp11 crayon curl data.table DBI digest doParallel dplyr dynamicTreeCut evaluate farver fastcluster fastmap fastmatch fgsea fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics ggplot2 ggrepel glue GO.db graph gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r latex2exp lattice lifecycle magrittr Matrix matrixStats memoise mime minpack.lm nnet openssl org.Hs.eg.db pillar pkgconfig png poweRlaw pracma preprocessCore R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack rlang rmarkdown rpart RSpectra rSpectral RSQLite rstudioapi S4Vectors S7 sass scales Seqinfo snow stringi stringr survival sys tibble tidyselect tinytex utf8 vctrs viridis viridisLite WGCNA withr xfun XVector yaml

BioNAR: Biological Network Analysis in R

Rendered fromBioNAR_overview.Rmdusingknitr::rmarkdown

Last update: 2025-02-26
Started: 2022-10-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Copy edge attributes from one graph to another	addEdgeAtts
Annotate Human Gene Names	annotateGeneNames
Add GO BP annotation to the graph vertices	annotateGoBP
Add GO CC annotation to the graph vertices	annotateGoCC
Add GO MF annotation to the graph vertices	annotateGoMF
Annotate nodes with GO terms	annotateGOont
Add InterPro Family and Domain annotation to the graph vertices	annotateInterpro
Add presynaptic functional groups	annotatePresynaptic
Add SCHanno synaptic functional groups	annotateSCHanno
Annotate graph with disease terms	annotateTopOntoOVG
Generic annotation function	annotateVertex
Add attributes to the vertex.	applpMatrixToGraph
BioNAR: Biological Network Analysis in R	BioNAR-package BioNAR
Build network from data.table	buildNetwork
Calculate memberships for all clustering algorithms and store them on the graph vertices.	calcAllClustering
Helper function that uses 'getBridgeness' to calculate graph node bridgeness values for selected algorithm and consensus matrix and save them as a graph attribute 'BRIDGENESS.<alg>' with '<alg>' replaced by the selected algorithm name.	calcBridgeness
Calculate the vertex centrality measures	calcCentrality
Function to calculate a distance matrix between a list of permuted vertex centrality matrices and a unperturbed reference matrix.	calcCentralityExternalDistances
Function calculates a set of distance metrics between each vertex pair given a list of vertex centrality matrices	calcCentralityInternalDistances
Calculate community membership for given clustering algorithm and store the results as new vertex attributes in the graph..	calcClustering
Calculate each disease-disease pair overlap given a list of disease terms.	calcDiseasePairs
Calculate the graph entropy for each perturbed vertex, and save the results as new vertex attributes in the graph.	calcEntropy
Calculate cluster memberships for the graph.	calcMembership
Hierarchical graph clustering	calcReclusterMatrix
Calculate sparsness of the graph.	calcSparsness
Matrix of cluster characteristics	clusteringSummary
Calculate annotation enrichment for clusters in the graph	clusterORA
Calculate cluster memberships for one of the graph component.	compMembership
Prepare mapping for degree-aware annotation shuffling.	degreeBinnedGDAs
Barabasi's Diseasome Network	diseasome
Escapes elements of list in annotation.	escapeAnnotation
Compare distance distributions of internal and external distances	evalCentralitySignificance
Find Largest Connected Component of the graph	findLCC
Fit Power Law to degree distribution.	fitDegree
Fit Fold-enrichment distribution to sigmoid function	fitSigmoid
Human Gene Disease Associations (GDA)	flatfile_human_gene2HDO.csv
Annotation from Gene Ontology Biological Process (GO_BP)	flatfile.go.BP.csv
Annotation from Gene Ontology Cellular Compartment (GO_CC)	flatfile.go.CC.csv
Annotation from Gene Ontology Molecular Function (GO_MF)	flatfile.go.MF.csv
Extract unique values from annotations.	getAnnotationList
Return vertex list for each term in annotation attribute	getAnnotationVertexList
Calculate bridginess from consensus matrix	getBridgeness
Calculate centrality measures for graph nodes.	getCentralityMatrix
Get clustering results for the graph.	getClustering
Return induced subgraph for cluster	getClusterSubgraphByID
Create new graph with communities as a nodes.	getCommunityGraph
Get HDO disease IDs	getDiseases
Get DiseaseTypes	getDType
Calculate DYNAMO sensitivity matrix.	getDYNAMO
Calculates vertex perturbation graph entropy.	getEntropy
Calculate the maximum entropy rate and initial entropy rate .	getEntropyRate
Generate random graph from reference	getGNP
Convert centrality matrix into ECDF	getGraphCentralityECDF
Utility function to get vertex ids from vertex attributes The function obtain attribute values and check duplicates in it. It fails if any duplicate found.	getIDs
Generate random graph from reference	getPA
Centrality measures for random graphs induced by input one	getRandomGraphCentrality
Calculate cluster robustness from consensus matrix	getRobustness
Goodnes of fit KS test	gofs
Result of PawerLaw fit	law-class
Calculate layout based upon membership	layoutByCluster
Calculate two-level layout from recluster matrix	layoutByRecluster
Function to make random resampling consensus matrix in memory	makeConsensusMatrix
Create membership 'data.frame' from graph for arbitrary annotation	makeMembership
Calculates bow-tie decomposition and marks vertices with one of the following in the 'BowTie' attribute: • SCC - maximal strong connected component; • IN - vertices not in SCC, but SCC is reachable from them; • OUT - vertices not in SCC, but reachable from SCC; • TU - vertices not in all three above, but reachable from IN and OUT is reachable from them (TUBES); • IDR - vertices not in SCC, but they are reachable from IN and OUT is NOT reachable from them (INTENDRILS); • ODR - vertices not is SCC, but they are NOT reachable from IN and OUT is reachable from them (OUTTENDRILS); • OTR - all other vertices.	markBowTie
Convert sparce matrix into triplet 'data.frame'.	metlMatrix
Calculates the normalised network modularity value.	normModularity
Randomly shuffle annotations	permute
Plot Bridgeness values	plotBridgeness
Plot graph entropy values versus vertex degree for each perturbed vertex value.	plotEntropy
Plot fraction of enriched communities	plotRatio
Plot results of the sigmoid fit	plotSigmoid
Table of protein protein interactions for presynaptic compartment	PPI_Presynaptic.csv
PPI graph for presynaptic compartment	PPI_Presynaptic.gml
Function to return vertex annotation from a graph in the Vertex Annotation form and format it for further analysis.	prepareGDA
Presynaptic genes specific functional annotation	PresynAn.csv
Hierarchical graph clustering	recluster
Remove vertex property.	removeVertexTerm
Calculate disease-disease pair overlaps on permuted network to estimate its statistical significance	runPermDisease
Function to randomly shuffle vertex annotation terms, whilst preserving the vertex degree originally found with that annotation term..	sampleDegBinnedGDA
Perturbe graph and calculate its clustering	sampleGraphClust
Schizopherina related synaptic gene functional annotation.	SCH_flatfile.csv
Calculate summary statistics from enrichment table	summaryStats
Unescape annotation strings	unescapeAnnotation
Auxiliary function to replace NAs with zeros.	zeroNA

Package: BioNAR 1.15.0

BioNAR: Biological Network Analysis in R

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)