NFP: Network Fingerprint Framework in R

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An implementation of the network fingerprint framework that introduced in paper "Network fingerprint: a knowledge-based characterization of biomedical networks" (Cui, 2015) <doi:10.1038/srep13286>. This method worked by making systematic comparisons to a set of well-studied "basic networks", measuring both the functional and topological similarity. A biological could be characterized as a spectrum-like vector consisting of similarities to basic networks. It shows great potential in biological network study.

Author
Yang Cao [aut, cre], Fei Li [aut]
Date of publication
2016-11-21 12:01:34
Maintainer
Yang Cao <yiluheihei@gmail.com>
License
GPL (>= 2)
Version
0.99.2
URLs

View on CRAN

Man pages

calc_sim_score
Calculating the similarity scores
cluster_info-methods
Extract the cluster information of _NFP_.
group-methods
Group information of _NFPRefnet_
install_data_package
Install NFP data package NFPdata
kegg_refnet
Human KEGG signal pathway maps
load_KEGG_refnet
Load the the reference molecular networks
net-methods
Basic networks of _NFPRefnet_ class
NFP
The NFP package
NFP-class
'NFP-class'
NFPRefnet-class
'NFPRefnet-class'
perm_score-methods
Extract the randomized similarity score
plot_NFPlist
Plot multiple NFPs.
plot_NFP-methods
Plot NFP results
refnet_name-methods
Names of basic networks
show-methods
The show generic function
show_NFPRefnet-methods
Show an Object
subnet-methods
Subset the basic networks
sub_NFP-methods
subset of NFP object

Files in this package

NFP
NFP/inst
NFP/inst/extdata
NFP/inst/extdata/signalPathway.txt
NFP/inst/extdata/humanPathway.txt
NFP/inst/doc
NFP/inst/doc/NFP.pdf
NFP/inst/doc/NFP.Rnw
NFP/inst/doc/NFP.R
NFP/tests
NFP/tests/testthat.R
NFP/tests/testthat
NFP/tests/testthat/test-NFP.R
NFP/tests/testthat/test-NFPRefnet.R
NFP/NAMESPACE
NFP/data
NFP/data/datalist
NFP/data/kegg_refnet.rda
NFP/R
NFP/R/NFP-class.R
NFP/R/Untitled.R
NFP/R/load_KEGG_refnet.R
NFP/R/kegg_refnet.R
NFP/R/plot_NFPlist.R
NFP/R/NFP.R
NFP/R/calc_sim_score.R
NFP/R/install_data_package.R
NFP/R/zzz.R
NFP/R/NFPRefnet-class.R
NFP/vignettes
NFP/vignettes/NFP.Rnw
NFP/vignettes/nfp_plot.png
NFP/README.md
NFP/MD5
NFP/build
NFP/build/vignette.rds
NFP/DESCRIPTION
NFP/man
NFP/man/NFPRefnet-class.Rd
NFP/man/cluster_info-methods.Rd
NFP/man/calc_sim_score.Rd
NFP/man/NFP-class.Rd
NFP/man/net-methods.Rd
NFP/man/show_NFPRefnet-methods.Rd
NFP/man/plot_NFPlist.Rd
NFP/man/load_KEGG_refnet.Rd
NFP/man/kegg_refnet.Rd
NFP/man/subnet-methods.Rd
NFP/man/perm_score-methods.Rd
NFP/man/group-methods.Rd
NFP/man/sub_NFP-methods.Rd
NFP/man/NFP.Rd
NFP/man/install_data_package.Rd
NFP/man/plot_NFP-methods.Rd
NFP/man/refnet_name-methods.Rd
NFP/man/show-methods.Rd