ProNet: Biological Network Construction, Visualization and Analyses

High-throughput experiments are now widely used in biological researches, which improves both the quality and quantity of omics data. Network-based presentation of these data has become a popular way in data analyses. This package mainly provides functions for biological network construction, visualization and analyses. Networks can be constructed either from experimental data or from a set of proteins and integrated PPI database. Based on them, users can perform traditional visualization, along with the subcellular localization based ones for Homo sapiens and Arabidopsis thaliana. Furthermore, analyses including topological statistics, functional module clustering and go profiling can also be achieved.

Author
Xiang-Yun Wu and Xia-Yu Xia
Date of publication
2015-10-22 22:14:27
Maintainer
Xia-Yu Xia <xiaxiayu.thu@hotmail.com>
License
GPL (>= 2)
Version
1.0.0

View on CRAN

Man pages

assemble
Operation of networks
ath
Arabidopsis thaliana Biogrid PPI database
cluster
Network clustering
comp.rand.subnet
Comparing a sub network to the randomly simulated ones
comp.subnet
Comparing a sub network to the whole one
construction
Network construction
construct_local
Local network construction
construct_nlocal
Non-local network construction
enrichment.annotation
GO enrichment annotation
extraction
Subnetwork extraction
GO_component
GO component annotation database
GO_function
GO function annotation database
GO_process
GO process annotation database
go.profiles
GO enrichment comparison
graph.add
Network union
HPRD
HPRD PPI database
human
Homo sapiens Biogrid PPI database
location
Hierarchical plot of biological network
locDB
Gene products' location database
mcode
MCODE network clustering
net.attack
Network attack
net.comparing
Comparing two networks
net.robustness
Network robustness
ProNet-package
Biological Network Construction, Visulization and Analyses
topology
Network topology analysis
topology_anc
Average neighborhood connectivity statistics
topology_betweenness
Betweenness statistics
topology_closeness
Closeness statistics
topology_cluster_coeffi
Clustering coefficient statistics
topology_degree
Degree statistics
topology_ec
Eigenvector centrality statistics
topology_shortest_paths
Shortest path statistics
topology_simple
Basic statistics
visualization
Network visualization

Files in this package

ProNet
ProNet/inst
ProNet/inst/example
ProNet/inst/example/hprd.id.txt
ProNet/inst/example/host.txt
ProNet/inst/example/iav.txt
ProNet/inst/doc
ProNet/inst/doc/Tutorial.R
ProNet/inst/doc/Tutorial.pdf
ProNet/inst/doc/Tutorial.Rnw
ProNet/src
ProNet/src/Makevars
ProNet/src/complex.c
ProNet/src/Makevars.win
ProNet/NAMESPACE
ProNet/data
ProNet/data/human.rda
ProNet/data/ath.rda
ProNet/data/HPRD.rda
ProNet/data/GO_component.rda
ProNet/data/locDB.rda
ProNet/data/datalist
ProNet/data/GO_function.rda
ProNet/data/GO_process.rda
ProNet/R
ProNet/R/GO_process.R
ProNet/R/topology.R
ProNet/R/GO_component.R
ProNet/R/GO_function.R
ProNet/R/human.R
ProNet/R/assemble.R
ProNet/R/construction.R
ProNet/R/comp.rand.subnet.R
ProNet/R/visualization.R
ProNet/R/ath.R
ProNet/R/enrichment.annotation.R
ProNet/R/comp.subnet.R
ProNet/R/go.profiles.R
ProNet/R/locDB.R
ProNet/R/clustering.R
ProNet/R/net.comparing.R
ProNet/R/location.R
ProNet/R/net.attack.R
ProNet/R/extraction.R
ProNet/R/HPRD.R
ProNet/R/MCODE.R
ProNet/R/net.robustness.R
ProNet/vignettes
ProNet/vignettes/cluster1.png
ProNet/vignettes/Degree.png
ProNet/vignettes/Location.png
ProNet/vignettes/Simple.png
ProNet/vignettes/go1.png
ProNet/vignettes/Length.png
ProNet/vignettes/Pathlen.png
ProNet/vignettes/go1vs2.png
ProNet/vignettes/Tutorial.Rnw
ProNet/MD5
ProNet/build
ProNet/build/vignette.rds
ProNet/DESCRIPTION
ProNet/man
ProNet/man/human.Rd
ProNet/man/topology_cluster_coeffi.Rd
ProNet/man/net.robustness.Rd
ProNet/man/assemble.Rd
ProNet/man/GO_component.Rd
ProNet/man/construct_local.Rd
ProNet/man/comp.rand.subnet.Rd
ProNet/man/locDB.Rd
ProNet/man/cluster.Rd
ProNet/man/construct_nlocal.Rd
ProNet/man/construction.Rd
ProNet/man/mcode.Rd
ProNet/man/comp.subnet.Rd
ProNet/man/topology.Rd
ProNet/man/GO_process.Rd
ProNet/man/ath.Rd
ProNet/man/ProNet-package.Rd
ProNet/man/topology_simple.Rd
ProNet/man/topology_betweenness.Rd
ProNet/man/go.profiles.Rd
ProNet/man/net.attack.Rd
ProNet/man/net.comparing.Rd
ProNet/man/topology_anc.Rd
ProNet/man/location.Rd
ProNet/man/visualization.Rd
ProNet/man/topology_degree.Rd
ProNet/man/HPRD.Rd
ProNet/man/enrichment.annotation.Rd
ProNet/man/extraction.Rd
ProNet/man/topology_ec.Rd
ProNet/man/topology_closeness.Rd
ProNet/man/graph.add.Rd
ProNet/man/topology_shortest_paths.Rd
ProNet/man/GO_function.Rd