Gene-Cluster-Shinny-App

Gene Cluster Shiny Application using RnaSeq files and Go.Db Kegg.Db and Biomart characteristics

This is a shiny Application that gives you the opportunity to use an RnaSeq file , enrich this dataset with specific characteristcs of those genes using Go.Db, Kegg.Db and Biomart , in order to cluster this with three different algorithms (kmodes,kproto,kmeans for every different)

The basic steps that this application has are:

The user inserts a RnaSeq file with row names the ensembl ids of genes and as data integer and normalized values choosing the right separation
After that he has to choose one or more variables he wants to add in his data. These attributes areQ:
- Terms from Go.db
- Orthology,Pathway and Motif from Kegg.Db
- Band,Gene biotype and Transript count from Biomart
Wait until the Upload and the execution of the algorithms After that there will be three different data sets, one with arithmetical data,one with categorical and one with mixed type data These will be used for kmeans,kmodes and kproto respectively
Then choose the algorithm and the parameters he wants in order to show the graphs and the visualization of the results
Finally the visualization must be refered, and they are:
- Arithmetical analysis of every cluster with boxplots
- Categorical analysis of every cluster
- Upset diagram for genes with common gcharacteristics
- Sankey diagram for comon genes between the clusters
- Graphs showing the evaluation metrics of every clustering

The packages you will need are in a command( you need the latest Rstudio version):

load.lib<-c("BiocManager", "shiny", "networkD3", "shinybusy",  "UpSetR", "dplyr",  "DT", "klaR" ,"clustMixType" ,"cluster" ,"readr" ,"Rtsne")

install.lib<-load.lib[!load.lib %in% installed.packages()]

for(lib in install.lib) install.packages(lib,dependencies=TRUE)




if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")
    
BiocManager::install("Organism.dplyr")

BiocManager::install("GenomicRanges")

BiocManager::install("KEGGREST")

BiocManager::install("AnnotationDbi")

BiocManager::install("GO.db")

BiocManager::install("hugene20sttranscriptcluster.db")

BiocManager::install("biomaRt")

BiocManager::install("org.Hs.eg.db")

BiocManager::install("DESeq2")

BiocManager::install("BiocGenerics")

BiocManager::install("Biobase")


library(shiny)

library(networkD3)

library(shinybusy)

library(AnnotationDbi)

library(org.Hs.eg.db)

library(hugene20sttranscriptcluster.db)
library(GO.db)

library(KEGGREST)

library(UpSetR)

library(cluster)

library(dplyr)

library(readr)

library(Rtsne)

library(DESeq2)


library(BiocGenerics)
library(biomaRt)

library(Biobase)

library(DT)

dimiapos/Gene-Cluster-Shinny-App

Gene-Cluster-Shinny-App