septic_shock_metaanalysis

This repository contains the code for the project:

Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock

Samanwoy Mukhopadhyay,Pravat K. Thatoi,Abhay D. Pandey,Bidyut K. Das,Balachandran Ravindran,Samsiddhi Bhattacharjee,Saroj K. Mohapatra

Availability of data

The dataset(s) and the R code supporting the conclusions of this article are available under the project ssnibmg in figshare https://doi.org/10.6084/m9.figshare.4592800.v1.

Step 1: Installation of the Data Package ssnibmg

1. Dowload the file ssnibmg_1.0.tar.gz from https://figshare.com/ (search for ssnibmg)
2. Change the directory to where you saved the file. Start R.
3. At the R prompt, issue the following command:

install.packages(pkgs=”ssnibmg_1.0.tar.gz”, repos=NULL)

4. Now the data package ssnibmg is installed on your computer.
5. Check with the following command:

library(“ssnibmg”)

Step 2: Running the analysis code

6. Dowload the file ssnibmgdoc.zip from https://figshare.com/ (search for ssnibmg)
7. Save the file at a suitable location and extract the contents. Change into the newly created directory ssnibmgdoc.
8. The code for data analysis are listed in the vignette ssnibmg_vignette.pdf.
9. The Rcode and Metadata are subdirectories under ssnibmgdoc (your current working directory in R).
10. The vignette is a self-computable document. Run the R code in steps to reproduce the results described in the vignette.