Crit-Lab / COVID_clustering Public

Code and data for the manuscript "Transcriptomic clustering of critically ill COVID-19 patients"

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Name		Name	Last commit message	Last commit date
Latest commit History 24 Commits
LICENSE		LICENSE
README.md		README.md
covid_clustering.R		covid_clustering.R
miRNA_counts.csv		miRNA_counts.csv
molecules_downnetwork.txt		molecules_downnetwork.txt
molecules_upnetwork.txt		molecules_upnetwork.txt
transcript_data.RData		transcript_data.RData

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COVID clustering

This folder contains all the data and code used in the manuscript entitled "Transcriptomic clustering of critically ill COVID-19 patients":

"COVID_clustering_final.R": R code. This file uploads all the following data files, that must be in the same directory.
"transcript_data.Rdata": Transcriptomic data. FastQ files available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197204.
"miRNA_counts.csv": miRNA raw counts. FastQ files available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197258.
"molecules_downnetwork.txt": Results from Ingenuity Pathway Analysys.
"molecules_upnetwork.txt": Results from Ingenuity Pathway Analysys.
"clinical_data_github.csv": Anonymized clinical data.