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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("dSimer")
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)
Version1.0.0

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

Functions

BOG Man page
CosineDFV Man page
d2g_fundo_entrezid Man page
d2g_fundo_symbol Man page
d2go_sample Man page
d2g_separation Man page
d2s_hsdn Man page
d2s_hsdn_sample Man page
dSimer Man page
dSimer-package Man page
FunSim Man page
get_GOterm2GeneAssos Man page
go2g_sample Man page
graphlet_sig_hprd Man page
HumanNet_sample Man page
HypergeometricTest Man page
ICod Man page
InformationContent Man page
interactome Man page
jaccardindex Man page
LLSn2List Man page
Normalize Man page
orbit_dependency_count Man page
plot_bipartite Man page
plot_heatmap Man page
plot_net Man page
plot_topo Man page
PPI_HPRD Man page
PSB Man page
Separation Man page
Separation2Similarity Man page
setWeight Man page
Sun_annotation Man page
Sun_function Man page
Sun_topology Man page
weight Man page
x2y_conv2_y2x Man page
x2y_df2list Man page

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

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