This folder contains all the data and code used in the manuscript entitled "Transcriptomic clustering of critically ill COVID-19 patients", published in the European Respiratory Journal (https://erj.ersjournals.com/content/early/2022/08/25/13993003.00592-2022). The preprint is available at https://www.medrxiv.org/content/10.1101/2022.03.01.22271576v1.
The folder contains the following files:
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"covid_clustering.R": R code. This file uploads all the following data files, that must be in the same directory.
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"transcript_data.Rdata": Transcriptomic data. FastQ files available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197204.
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"transcript_data_trt.Rdata": Transcriptomic data at ICU day 4. FastQ files available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206264.
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"miRNA_counts.csv": miRNA raw counts. FastQ files available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197258.
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"molecules_downnetwork.txt": Results from Ingenuity Pathway Analysys.
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"molecules_upnetwork.txt": Results from Ingenuity Pathway Analysys.
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"clinical_data.csv": Anonymized clinical data.
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"index_data_trt.csv": File containing cluster and treatment received by patients with a Day 4 transcriptome.
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Cecilia López-Martínez (clm@crit-lab.org), Guillermo M Albaiceta (gma@crit-lab.org), Laura Amado-Rodríguez (lar@crit-lab.org).