This repository contains the scripts and additional files necessary to replicate the findings of the study SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity. The data have been deposited with links to BioProject accession number PRJNA982620.
- Unitas (v.1.8.0).
- Bowtie (v.1.3.1).
- Scram (v.0.2.2).
- Centrifuge (v.1.0.4).
- R (v.4.2.2).
- Python >= 3.8.
- Biopython, numpy, pandas, argparse, multiprocessing, itertools.
- rgl, knitr, tidyverse, factoextra, ggfortify, DESeq2, ggsci, ggExtra, Biostrings, ggdist, scales, ggbreak.
Please refer to the specific scripts and their descriptions for detailed information on how to replicate the findings of the study. The additional files needed are provided in Additional_data
. Database and genome versions used for classification can be found in the Material and Methods section.