unistbig / gscluster

gene-set clustering and network visualization

GScluster is a standalone Shiny/R package for network-weighted gene-set clustering and network visualization.

Installation

Open R program and type following commands in R console.

install.packages('devtools')
library(devtools)
install_github('unistbig/GScluster')
library(GScluster)

Example Run

To run demo file, please type following R code.

GScluster()

To run user's own data, please modify following example R codes.

1. Read gene-set analysis result table.
   

GSAresult=read.delim('https://github.com/unistbig/GScluster/raw/master/sample_geneset.txt', stringsAsFactors=FALSE)

2. Read gene score table.
   

GeneScores=read.delim('https://github.com/unistbig/GScluster/raw/master/sample_genescore.txt', header=F)

3. Run GScluster
   

GScluster(GSAresult = GSAresult, GeneScores = GeneScores, Species = 'H', alpha = 1, GsQCutoff = 0.25, GQCutoff = 0.05)

User's Manual

User's manual is available here.

Example data download

• Type 2 Diabetes Mellitus Data (DIAGRAM)
  Gene-set analysis result file (q-value cutoff: 0.25)
  Genescore file (q-value cutoff: 0.01)
  

• Colon Cancer Data
  Gene-set ananlysis result file (q-value cutoff: 0.01)
  Genescore file (q-value cutoff: 0.01)
  

• Acute Myeloid Leukemia (AML) Data
  Gene-set ananlysis result file (q-value cutoff: 0.01)
  Genescore file (q-value cutoff: 0.01)
  

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Running time of GScluster is shown below for different numbers of input gene-sets.

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Contact: Dougu Nam ([email protected])
Any feedback or comments are greatly appreciated!!

gscluster's Issues

'score' should be 'Score' on line 31 of GetGSASeqData()

Hopefully an easy fix ;)

'score' should be 'Score' on GetGSASeqData()

Otherwise this error results:
Error in read.delim(score, stringsAsFactors = FALSE) :
object 'score' not found

GScluster/R/GetGSASeqData.R

Line 31 in 7e4146f

tab <- read.delim(score, stringsAsFactors = FALSE)

Error in buildNode

Hello,

I've been trying to run the GScluster function and had been running up against an error. Finally, I tried just running the sample code and got the same error, so I'm wondering what I can do to troubleshoot:

`data=GetGSASNP2Data(filename='https://github.com/unistbig/GScluster/raw/master/inst/GScluster/GSASNP2_DIAGRAM.txt')
GSAresult = data$GSAresult
GeneScores = data$GeneScores
GScluster(GSAresult = GSAresult, GeneScores = GeneScores, Species = 'H', alpha = 1, GsQCutoff = 0.25, GQCutoff = 0.05)
[1] "PPI table is not given, STRING data is used."

Listening on http://127.0.0.1:7313
Warning: Error in buildNode: id must be string
53: stop
52: buildNode
51: RenderGeneSetNetwork [/usr/local/lib/R/3.6/site-library/GScluster/GScluster/app.R#1262]
50: server [/usr/local/lib/R/3.6/site-library/GScluster/GScluster/app.R#1289]
Error in buildNode(id = nodes[i, 1], bgColor = nodes[i, 3], labelColor = "black", :
id must be string`

Any input would be really appreciated.

Thanks,
Jim

Error from shinyjs

Hi, I'm getting the following error from running the demo, as well as the example data:

> GScluster()
[1] "run example data"
[1] "PPI table is not given, STRING data is used."
Loading required package: Matrix
Error: shinyjs: extendShinyjs: `functions` argument must be provided. 

I just installed shinyjs, maybe it is a version issue or something? Here's part of my sessionInfo:

other attached packages:
 [1] Matrix_1.2-18         shinyCyJS_0.0.9       GScluster_1.1.9       V8_3.2.0              wordcloud2_0.2.1     
 [6] tm_0.7-7              NLP_0.2-0             shinyWidgets_0.5.3    shinyjs_2.0.0         shinydashboard_0.7.1 
[11] shinycssloaders_1.0.0 shiny_1.5.0           igraph_1.2.5          htmlwidgets_1.5.2     DT_0.15

thanks!

Error In Installation

Hi,
I am getting an error while I am trying to install GScluster.
I am following the instruction by running "remotes::install_github('unistbig/GScluster')".
Following is the error.
Error: (converted from warning) package 'DT' was built under R version 4.0.3
Execution halted
ERROR: lazy loading failed for package 'GScluster'
Can you please help on this?
Also is it possible to upload the tar file so that I can try installing it from source?