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SurprisalAnalysis R package guidelines

🖥️ Installation

To install the R package:

install.packages('devtools')
devtools::install_github('AnniceNajafi/SurprisalAnalysis')

Usage

To use the R package you should follow the steps below:

I. Store gene expression data in a csv file with the first row holding the sample names and the first column holding the gene names.
  1. Read the csv file and run the following code: 
  input.data <- read.csv('expression_data.csv')
  results <- surprisal_analysis(input.data)
  1. To run GO analysis on the patterns simply use the code below:

results[[2]]-> transcript_weights
percentile_GO <- 0.95 #change based on your preference
lambda_no <- 1 #change based on your preference
GO_analysis_surprisal_analysis(transcript_weights, percentile_GO, lambda_no, key_type = "SYMBOL", flip = FALSE, species.db.str =  "org.Hs.eg.db", top_GO_terms=15)

Use GUI from R package

Simply run the following code:

runSurprisalApp()

Web-based application

A web-based application based on the above has been deployed on this link.

Open source disclaimer

This is an open-source project based on a previously developed methodology. Requests or attempts on the expansion and further improvement of the code is welcome and encouraged.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.