README.md

In GScluster/application: Plot clustered Geneset Network

GScluster Appication README

How to Use :

library(devtools)
install_github('GScluster/application')
library(application)
library(shiny)

Additionally, GScluster needs R library from CRAN( shinydashboard, shinyjs, DT, V8 ) and from Github (r-cytoscape.js). which can be installed using this code.

Important notice

r-cytoscape.js is being updated. (https://github.com/cytoscape/cyjShiny) user need to install legacy package manually. from this link *https://github.com/cytoscape/cyjShiny/archive/v0.0.7.tar.gz *

install.packages('shiny')
install.packages('shinydashboard')
install.packages('shinyjs') 
install.packages('DT')
install.packages('V8')
install.packages('devtools')
install.packages('cyjShiny-0.0.7.tar.gz',repos = NULL) # manually install

# devtools::install_github("cytoscape/r-cytoscape.js")
# not available

GScluster is network Analysis & Visualize tool for GSA results. It provides visualized result of Clustered Gene-set and their sub-network. Initially, GScluster Application (call App) provides only application frame, So to run this App, it's required to download PPI data by species. once PPI data downloaded, it will installed in user's, and it doesn't need to download again.

Important Downloading Data may fails according to network status between user and github. If PPI files can't be downloaded using R automatically, user can download them by manually.

Download additional data from github.com/GScluster/data and locate it to "package directory"/data/"Species" for example : "C:\Program Files\R\R-3.4.3\library\application\data\human" after that GScluster App will run without problem.

GScluster App provides 9 species, that is Arabidopsis, C.elegans, E.coli, Fly, Human, Mouse, Rat, Yeast, Zebra fish.

TRY DEMO, will load Human sample data and run GScluster automatically which can be downloaded in Downloads tab also

GScluster includes manual and sample datas itself

Data format :

Geneset File ( Required )

Geneset File consisted with tab-delimited 3 column txt file. (including Header) Each column is Geneset Name, Gene member in set, Geneset Qvalue. Gene member should separated by space.

Example

GS GeneList Qvalues GENESET1 RAPGEF3 CDX2 AGPAT1 GNB5 0.005412803 GENESET2 ALB PCK1 BDH1 HNF1A NF1 0.005412803 GENESET3 AGPAT1 AGPAT2 AGPAT6 0.005412803 ....

Genescore File ( Optinoal, but recommended )

Genescore File consisted with tab-delimited 2 column txt file. (not include Header) Each columns is Gene, Pvalue ( or Qvalue ) Score should be raw ( not log scale, 0 ~ 1) and Gene should be Symbol.

Example

TCF7L2 1e-06 MTNR1B 1e-06 RPSAP52 1e-06 FTO 1e-06 IGF2BP2 1e-06 ....

notice that Gene, can take either Gene Symbol or Entrez id or Ensembl form Some species (Arabidopsis / Ecoli / Yeast) doesn't handle Ensembl type

GScluster/application documentation built on May 18, 2019, 2:37 a.m.