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.

Install the latest version of this package by entering the following in R:
install.packages("ProNet")
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

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

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

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

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