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.

AuthorXiang-Yun Wu and Xia-Yu Xia
Date of publication2015-10-22 22:14:27
MaintainerXia-Yu Xia <xiaxiayu.thu@hotmail.com>
LicenseGPL (>= 2)
Version1.0.0

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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

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