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

View on CRAN

Functions

assemble Man page
ath Man page
cluster Man page
comp.rand.subnet Man page
comp.subnet Man page
construction Man page
construct_local Man page
construct_nlocal Man page
enrichment.annotation Man page
extraction Man page
GO_component Man page
GO_function Man page
GO_process Man page
go.profiles Man page
graph.add Man page
HPRD Man page
human Man page
location Man page
locDB Man page
mcode Man page
net.attack Man page
net.comparing Man page
net.robustness Man page
ProNet Man page
ProNet-package Man page
topology Man page
topology_anc Man page
topology_betweenness Man page
topology_closeness Man page
topology_cluster_coeffi Man page
topology_degree Man page
topology_ec Man page
topology_shortest_paths Man page
topology_simple Man page
visualization Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.