dSimer: Integration of Disease Similarity Methods
Version 1.2.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorMin Li <limin@mail.csu.edu.cn>, Peng Ni <nipeng@csu.edu.cn> with contributions from Zhihui Fei and Ping Huang.
Bioconductor views Network Software Visualization
Date of publicationNone
MaintainerPeng Ni <nipeng@csu.edu.cn>
LicenseGPL (>= 2)
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("dSimer")

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

Functions

BOG Man page Source code
BOG_normat_cpp Source code
BOG_simmat_cpp Source code
CosineDFV Man page Source code
FindOneDiseaseAssoGOterms Source code
FunSim Man page Source code
FunSim_onepair Source code
HumanNet_sample Man page
HypergeometricTest Man page Source code
HypergeometricTest_onedisease Source code
HypergeometricTest_onedisease_onego Source code
ICod Man page Source code
ICod_onepair Source code
ICod_onepair_cpp Source code
InformationContent Man page Source code
LLSn2List Man page Source code
MultipleTesting Source code
Normalize Man page Source code
NormalizingFactor Source code
NormalizingFactor_single Source code
PPI_HPRD Man page
PSB Man page Source code
PSB_termsim_cpp Source code
Separation Man page Source code
Separation2Similarity Man page Source code
Sun_annotation Man page Source code
Sun_function Man page Source code
Sun_topology Man page Source code
Sun_topology_cpp Source code
TDistanceMat_cpp Source code
cal_disease_oneline_separation Source code
cal_disease_pair_separation Source code
cal_set_pair_distance Source code
cal_single_set_distance Source code
d2g_fundo_entrezid Man page
d2g_fundo_symbol Man page
d2g_separation Man page
d2go_sample Man page
d2s_hsdn Man page
d2s_hsdn_sample Man page
dSimer Man page
dSimer-package Man page
filterGO2Glists Source code
funsim Source code
get_GOterm2GeneAssos Man page Source code
go2g_full Source code
go2g_sample Man page
graphlet_sig_hprd Man page
informationContent Source code
interactome Man page
jaccardindex Man page Source code
jaccardindex_line Source code
modular Source code
orbit_dependency_count Man page
plot_bipartite Man page Source code
plot_heatmap Man page Source code
plot_net Man page Source code
plot_topo Man page Source code
psb_line Source code
psb_onepair Source code
setWeight Man page Source code
setdsim Source code
setidf Source code
settf Source code
sim_mat Source code
simplot Source code
termsim Source code
theme_dose Source code
weight Man page
x2y_conv2_y2x Man page Source code
x2y_df2list Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/BOG.R
R/CosineDFV.R
R/ICod.R
R/PSB.R
R/Plots.R
R/RcppExports.R
R/SemFunSim.R
R/Separation.R
R/Sun.R
R/common_use.R
R/dSimer-package.R
R/data_preprocess.R
README.md
build
build/vignette.rds
data
data/HumanNet_sample.rda
data/PPI_HPRD.rda
data/d2g_fundo_entrezid.rda
data/d2g_fundo_symbol.rda
data/d2g_separation.rda
data/d2go_sample.rda
data/d2s_hsdn.rda
data/d2s_hsdn_sample.rda
data/datalist
data/go2g_sample.rda
data/graphlet_sig_hprd.rda
data/interactome.rda
data/orbit_dependency_count.rda
data/weight.rda
inst
inst/NEWS
inst/doc
inst/doc/dSimer.R
inst/doc/dSimer.Rmd
inst/doc/dSimer.html
man
man/BOG.Rd
man/CosineDFV.Rd
man/FunSim.Rd
man/HumanNet_sample.Rd
man/HypergeometricTest.Rd
man/ICod.Rd
man/InformationContent.Rd
man/LLSn2List.Rd
man/Normalize.Rd
man/PPI_HPRD.Rd
man/PSB.Rd
man/Separation.Rd
man/Separation2Similarity.Rd
man/Sun_annotation.Rd
man/Sun_function.Rd
man/Sun_topology.Rd
man/d2g_fundo_entrezid.Rd
man/d2g_fundo_symbol.Rd
man/d2g_separation.Rd
man/d2go_sample.Rd
man/d2s_hsdn.Rd
man/d2s_hsdn_sample.Rd
man/dSimer-package.Rd
man/get_GOterm2GeneAssos.Rd
man/go2g_sample.Rd
man/graphlet_sig_hprd.Rd
man/interactome.Rd
man/jaccardindex.Rd
man/orbit_dependency_count.Rd
man/plot_bipartite.Rd
man/plot_heatmap.Rd
man/plot_net.Rd
man/plot_topo.Rd
man/setWeight.Rd
man/weight.Rd
man/x2y_conv2_y2x.Rd
man/x2y_df2list.Rd
src
src/BOG.cpp
src/GO2GeneAssos.cpp
src/ICod.cpp
src/PSB.cpp
src/R_dSimer_init.c
src/RcppExports.cpp
src/Sun.cpp
vignettes
vignettes/dSimer.Rmd
vignettes/nature.csl
dSimer documentation built on May 20, 2017, 9:39 p.m.