dSimer: Integration of Disease Similarity Methods

dSimer is an R package which provides computation of nine methods for measuring disease-disease similarity, including a standard cosine similarity measure and eight function-based methods. The disease similarity matrix obtained from these nine methods can be visualized through heatmap and network. Biological data widely used in disease-disease associations study are also provided by dSimer.

Author
Min Li <limin@mail.csu.edu.cn>, Peng Ni <nipeng@csu.edu.cn> with contributions from Zhihui Fei and Ping Huang.
Date of publication
None
Maintainer
Peng Ni <nipeng@csu.edu.cn>
License
GPL (>= 2)
Version
1.0.0

View on Bioconductor

Man pages

BOG
calculate disease similarity by BOG
CosineDFV
calculate disease similarity by using feature vectors
d2g_fundo_entrezid
d2g_fundo_entrezid
d2g_fundo_symbol
d2g_fundo_symbol
d2go_sample
d2go_sample
d2g_separation
d2g_separation
d2s_hsdn
d2s_hsdn
d2s_hsdn_sample
d2s_hsdn_sample
dSimer-package
Integration of Disease Similarity Methods
FunSim
calculate disease similarity by FunSim
get_GOterm2GeneAssos
get GO-gene associations
go2g_sample
go2g_sample
graphlet_sig_hprd
graphlet_sig_hprd
HumanNet_sample
HumanNet_sample
HypergeometricTest
Hypergeometric test and multiple testing
ICod
calculate disease similarity by ICod
InformationContent
calculating information content
interactome
interactome
jaccardindex
calculating Jaccard Index
LLSn2List
convert data.frame of HumanNet log-likelihood Score to list
Normalize
normalize data
orbit_dependency_count
orbit_dependency_count
plot_bipartite
plot disease-gene (or GO term etc.) associations as a...
plot_heatmap
similarity matrix heatmap plotting
plot_net
plot a network based on a symmetric disease similarity matrix
plot_topo
plot topological relationship of two gene sets
PPI_HPRD
PPI_HPRD
PSB
calculate disease similarity by PSB
Separation
calculating network-based separation of disease pairs
Separation2Similarity
a method which convert separation to similarity
setWeight
set weight factor
Sun_annotation
Sun's annotation measure of disease similarity calculating
Sun_function
Sun's function measure of disease similarity calculating
Sun_topology
Sun's topology measure of disease similarity calculating
weight
weight
x2y_conv2_y2x
convert x2ylist to y2xlist
x2y_df2list
convert x-y associations

Files in this package

dSimer/DESCRIPTION
dSimer/NAMESPACE
dSimer/R
dSimer/R/BOG.R
dSimer/R/CosineDFV.R
dSimer/R/ICod.R
dSimer/R/PSB.R
dSimer/R/Plots.R
dSimer/R/RcppExports.R
dSimer/R/SemFunSim.R
dSimer/R/Separation.R
dSimer/R/Sun.R
dSimer/R/common_use.R
dSimer/R/dSimer-package.R
dSimer/R/data_preprocess.R
dSimer/README.md
dSimer/build
dSimer/build/vignette.rds
dSimer/data
dSimer/data/HumanNet_sample.rda
dSimer/data/PPI_HPRD.rda
dSimer/data/d2g_fundo_entrezid.rda
dSimer/data/d2g_fundo_symbol.rda
dSimer/data/d2g_separation.rda
dSimer/data/d2go_sample.rda
dSimer/data/d2s_hsdn.rda
dSimer/data/d2s_hsdn_sample.rda
dSimer/data/datalist
dSimer/data/go2g_sample.rda
dSimer/data/graphlet_sig_hprd.rda
dSimer/data/interactome.rda
dSimer/data/orbit_dependency_count.rda
dSimer/data/weight.rda
dSimer/inst
dSimer/inst/NEWS
dSimer/inst/doc
dSimer/inst/doc/dSimer.R
dSimer/inst/doc/dSimer.Rmd
dSimer/inst/doc/dSimer.html
dSimer/man
dSimer/man/BOG.Rd
dSimer/man/CosineDFV.Rd
dSimer/man/FunSim.Rd
dSimer/man/HumanNet_sample.Rd
dSimer/man/HypergeometricTest.Rd
dSimer/man/ICod.Rd
dSimer/man/InformationContent.Rd
dSimer/man/LLSn2List.Rd
dSimer/man/Normalize.Rd
dSimer/man/PPI_HPRD.Rd
dSimer/man/PSB.Rd
dSimer/man/Separation.Rd
dSimer/man/Separation2Similarity.Rd
dSimer/man/Sun_annotation.Rd
dSimer/man/Sun_function.Rd
dSimer/man/Sun_topology.Rd
dSimer/man/d2g_fundo_entrezid.Rd
dSimer/man/d2g_fundo_symbol.Rd
dSimer/man/d2g_separation.Rd
dSimer/man/d2go_sample.Rd
dSimer/man/d2s_hsdn.Rd
dSimer/man/d2s_hsdn_sample.Rd
dSimer/man/dSimer-package.Rd
dSimer/man/get_GOterm2GeneAssos.Rd
dSimer/man/go2g_sample.Rd
dSimer/man/graphlet_sig_hprd.Rd
dSimer/man/interactome.Rd
dSimer/man/jaccardindex.Rd
dSimer/man/orbit_dependency_count.Rd
dSimer/man/plot_bipartite.Rd
dSimer/man/plot_heatmap.Rd
dSimer/man/plot_net.Rd
dSimer/man/plot_topo.Rd
dSimer/man/setWeight.Rd
dSimer/man/weight.Rd
dSimer/man/x2y_conv2_y2x.Rd
dSimer/man/x2y_df2list.Rd
dSimer/src
dSimer/src/BOG.cpp
dSimer/src/GO2GeneAssos.cpp
dSimer/src/ICod.cpp
dSimer/src/PSB.cpp
dSimer/src/R_dSimer_init.c
dSimer/src/RcppExports.cpp
dSimer/src/Sun.cpp
dSimer/vignettes
dSimer/vignettes/dSimer.Rmd
dSimer/vignettes/nature.csl