Palmitic Acid Upregulates Type I Interferon-Mediated Antiviral Response and Cholesterol Biosynthesis in Human Astrocytes

The following repository contains the notebooks and the libraries used to obtain the results of this article. All datasets and libraries are open sourced and free to use. If you use any of the following in your analysis, please cite them properly.

1. RNAseq-pipeline

A detailed report of the astrocyte transcriptome analysis is found with the rnaseq pipeline from nf-core, which is generated by MultiQC; a visualization tool that generates a single HTML report summarizing all samples in the project

2. Expression

Differential expression analysis was conducted using the bioconductor edgeR package. We used the gene-level counts matrix to identify significant differentially expressed genes (DEGs) across 12 comparisons

3. Overlapping

The identification of overlapping DEGs was conducted with the ggVennDiagram package through differentiating those that were significantly up- and down-regulated

4. Enrichment

It contains the functional enrichment results for human astrocytes. Over-representation analyses were performed using the clusterProfiler package implemented in R

5. PPI_network

PPI network was constructed from the STRING database using Cytoscape. From this network, we identified significant gene clustering modules and hub genes using the MCODE and Cytohubba plugins, respectively

6. Notebooks

All source code is in Rmarkdown style to run step by step all the analysis

Running analysis

1. Install R and R Studio if needed
2. Clone this repository
3. Install required R packages
4. Knit the R Markdown files in order

Bug Reports

Please report bugs through the GitHub issues system