The user interface TraitCorr allows to determine those genes that significantly correlate with a selected trait or among traits and provides various visualisation and analysis possibilities.
correlation of transcriptome data with trait information
Please find our manuscript published in Gene Reports TraitCorr-Gene-Report-Nussbaumer et al. 2020 and our preprint TraitCorr-Preprint-Nussbaumer et al., 2019
Following packages are needed, the Rscript "ReporteRs" has been replaced by R package "officer", as suggestd by davidgohel/ReporteRs.
library(d3heatmap)
library(gplots)
library(officer)
library(VennDiagram)
library(scales)
library(shiny)
library(shinyalert)
library(shinyBS)
library(shinyjs)
library(shinythemes)
library(xlsx)
This is how to run it:
source("methods.R")
source("ui.R")
source("server.R")
shinyApp(ui,server)
To simplify the process of running traitcorr we added the method run_traitcorr that includes all dependencies.
Normally, I would copy the content of run_traitCorr.R into the R workbench and then I first see whether R packages are still needed. If so, then the R shiny GUI should be displayed. The input_data "traitCorr_input.zip" would have to get extracted and finally the data can be included and afterwards possible to analyse the demo files.
run_traitcorr()