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.

AuthorMin Li <limin@mail.csu.edu.cn>, Peng Ni <nipeng@csu.edu.cn> with contributions from Zhihui Fei and Ping Huang.
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

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

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