Title: Total RNA sequencing reveals gene expression and microbial alterations shared by Oral pre-malignant Lesions and Cancer.

This code repo contains relevant data, scripts, and results for the PML project.

Analysis overview: A cohort of 66 patients' oral tissue was sequenced to obtain gene expression and microbial abundance profiles to study their transcriptome. The cohort was divided into four histopathological groups - control (normal mucosa), HkNR (hyperkeratosis; not reactive), dysplasia, and OSCC (oral squamous cell carcinoma). The key findings from this analysis are represented through this graphical abstract shown below:

Directory structure:
/scripts - all the relevant scripts and compiled (.html) files for the analysis.
/data - input data (expression data of host and microbes, annotation data, etc.,)
/results - all results from various methods.

A short description of analysis scripts:
00_summ_stats.{Rmd, html} - summary statistics and eset creation
01_imp_summary.{Rmd, html} - imputation to obtain smoking status for missing patients (n=11)
02_dimred_hvg.{Rmd, html} - Dimensionality reduction on gene expression data, clustering analysis, finding highly variable genes.
03_diffanalysis.{Rmd, html} - pairwise differential expression analysis using DESeq2 between histopathological groups.
04_hyper_gsva_sigs.{Rmd, html} - overrepresentation analysis using hypeR from the differentially expressed genes and GSVA enrichment analysis on relevant signatures.
05_immune_deconv.{Rmd, html} - Immune cell-type deconvolution analysis using CIBERSORT scores.
06_micro_analysis_msea.{Rmd, html} - Microbial abundance analysis and MSEA enrichment analysis.
07_microbiome_msea.{ipynb, html} - MSEA analysis using msets derived from published microbe-host genes compendium.