Methods In Molecular Biology_chapter

In this repository the code for coexpression and promoter analysis is provided. Before running through this tutorial, you must have latest version of R installed.

R installation

Following command can be use to install and update R on Ubuntu

#Update and Install R

sudo apt-get update

sudo apt-get install r-base r-base-dev

sudo apt-get upgrade

#Know R version

R --version

Running the Scripts

1. COEXPRESSION ANALYSIS: coexpression.R

   This R script requires two libraries RColorBrewer and gplots, and can be run from Ubuntu terminal like this

   Rscript coexpression.R tissue

The file tissue contains the expression value iin the form of RPKM (Reads per kilo base per million mapped reads)

After successful completeion, two files will be generated: This correlation matrix (tissue_coexpression_matrix.txt) and a heatmap (tissue.expression.pdf)

2. TRANSCRIPTION FACTOR BINDING SITE ANALYSIS: JASPAR.R

This R script requires following libraries TFBSTools, JASPAR2020, Biostrings, GenomicRanges, dplyr, ggplot2, and can be run from Ubuntu terminal like this

Rscript JASPAR.R G10Hpro

The file G10Hpro contains the promoter sequence in FASTA format. After successful completeion, a directory (G10Hpro.result ) with raw data, a table ( G10Hpro.result.csv ) and an image (G10Hpro.png ) file will be created.

Citation

Please cite this book chapter if you find these scripts useful for your work

For any question and comment, please email me - ssi228@uky.edu