I have results of differential gene expression analysis for both the human and bacterial RNAseq data. Further i would like to do correlation analysis to see if some genes from bacterial side correlate to human genes.

Since I am new to R and Correlation analysis, Could anybody share any pipeline on how to do so. I have found gene to gene correlation between different samples for a single specie but here I am trying to find correlation between the genes of two different species.

You can use the following pipeline in R:

Load the gene expression data for both human and bacterial samples into R. Filter the data to remove any genes that are not expressed in either the human or bacterial samples. Calculate the correlation between the human and bacterial gene expression data using the cor function in R. Identify any genes that have a significant correlation between the human and bacterial samples. Here is an example code snippet that demonstrates how to calculate the correlation between two sets of gene expression data in R:

Load the gene expression data

human_data <- read.csv("human_data.csv") bacterial_data <- read.csv("bacterial_data.csv")

Filter the data

human_data <- human_data[rowSums(human_data) > 0, ] bacterial_data <- bacterial_data[rowSums(bacterial_data) > 0, ]

Calculate the correlation

correlation <- cor(human_data, bacterial_data)

Identify significant correlations

significant_correlations <- which(correlation > 0.8)

This code will load the gene expression data for both human and bacterial samples, filter the data to remove any genes that are not expressed, calculate the correlation between the human and bacterial gene expression data, and identify any genes that have a significant correlation.

Reference: https://bmcbioinformatics.biomedcentral.com/articlesblossom word game/10.1186/s12859-021-04130-7 and https://news.harvard.edu/gazette/story/2021/05/study-links-genetic-makeup-of-bacteria-in-the-human-gut-to-several-diseases/